Project Beta and Omega
by blackstarlight17
Summary: Professor Sebastian is given a new research project, to assist with cloning other samples collected relating to Mew. As he works on it, he begins to question himself, his place, and most of all, begin to question what is best for the clones he comes to care for.
1. Chapter 1

_**I did my best trying to write this following the anime mostly, so if mistakes are found, please let me know so I may fix them.**_

 _ **There will be several pairings, some onesided, others known, some probably leaving you guessing.**_

 _ **There will be some OCs mentioned, some minor, others having larger roles.**_

 _ **The fic will get more mature in later chapters, so if you're not a fan of things such as lemon scenes, lots of swearing, rape, yaoi (guyxguy), then I suggest you move onto something different.**_

 _ **Posting will range between Thursday and Friday, sorry for not mentioning it sooner. Been up all night working on this among others. So those thinking you'll get another chapter soon, you'll have to wait another week. I hope you'll understand.**_

 _ **Other than that, hope you enjoy.**_

* * *

Carrying an envelope under his arm, Professor Sebastian slowly walked through the halls, completely exhausted. To be precise, he was suffering jet lag, the long flight not helping at all.

He had been given a call from his boss about a _slight_ change in his already busy work schedule. That usually meant he was being given even _more_ work to do, something he honestly didn't need nor want right now.

He had been running himself ragged already on five projects already dropped in his lap. It was a mix of either incompetence of the others, a new idea the boss came up, or all his better scientists were busy on secret projects where they couldn't be spared.

Part of him wanted to yell at Giovanni to cut him some slack, but held his tongue, preferring to continue living than having his throat slit or bullet in the head.

He may be one of Giovanni's favorites, one of his more reliable researchers, that didn't mean he isn't irreplaceable.

There are others who could do his work or find someone new to take his place whenever he felt like it. He isn't the _only_ scientist to specialize in evolution. It may not be an easy field, but it isn't impossible.

He's just as disposable as the grunts that work for the crime lord…

"I feel like I'm going to puke," he groaned, wishing the damn railway would finish he could stop flying.

He wasn't afraid of flying, oh no, he simply hated the whole thing by how chaotic and sickening it could become.

The airports and sometimes the planes themselves are crowded with dozens of noisy people and Pokémon, the former mostly.

There have been people who harassed him for a battle, not knowing he wasn't a trainer, just a scientist. Sometimes that ends up getting him caught in some random conversation, mostly ridiculous ones than anything meaningful.

If it isn't the people that make his mood sour, it's the plane itself, hating how stuffy it can get at times, having to listen to various noises. They could be someone eating loudly, children screaming because they're bored, scared, or cranky from lack of sleep. There could be some who are coughing and snorting, getting over colds or allergies, some getting airsick, the entire thing making _him_ feel sick.

Probably a good thing he refuses alcohol, he doesn't need to end up like them or worse. Same with any of the food that's served here, knowing most are either close to expiring or simply not his taste.

But what may really piss him off, sometimes enough to actually snap back, whether the conversation included him or not, are people who are thoughtlessly rude.

So what if a there's a same sex couple and they have a child, doesn't give anyone the right to talk shit about them!

Sure, he's an asshole, but at least he has _some_ class about it. He isn't going to act like some spoiled brat and demand things. If he doesn't like something, he'll either suck it up like a gentleman or politely ask to move to another spot.

It must make one wonder why he's willing to fly, to put up with all this, stressing himself out far more than he should.

He has two reasons for flying than finding some other means, although if the Magnet Train is ever completed, he'll tell Giovanni he's taking that from now on.

Fuck his free plane tickets, unless it was a life or death situation, he'll take a longer route to get to headquarters.

Hell, if he had the chance, he'd take a boat, even _walk_ to Kanto.

As for his reason for flying, one is because of Giovanni, the man has a short temper, having seen it flare more than he would like. It could be subtle or become an inferno at the snap of a finger. If he wants you somewhere, you better be there or risk enduring his very likely, fatal, wrath.

It was also because of that temper that helped control his own, having at times been at the wrong end of it in his early days working in Team Rocket.

Doesn't mean he _won't_ snap at someone if they screw up, making him look like an idiot, worse, making _Giovanni_ look like an idiot.

At least being a more favorable scientist has its perks, he's made head of most researches, so people rarely argue with him. Any that do are either those of a higher rank than his own or they actually _have_ something to contribute that could help.

Yes, he isn't so self-absorbed he'd ignore criticism, unlike others, he's willing to hear them out. He isn't perfect as others may assume him to be. He has flaws as does any other living creature with a brain. If it weren't for those flaws, mankind wouldn't have gotten as far as they have.

His other reason for flying is the chance to see his daughters…

Yes, he actually once had a family, been once married, had children with said wife, but she left him shortly after, deeming him useless and boring. And to add salt to the wound, she took his girls away, not telling him where, having them raised by her or some other to become agents.

That was another thing he could tolerate, children, he may get annoyed if a child is rude and they're old enough to know better.

But for the real little ones he'll let it slide. They don't know better and need to be shown the proper way to act than simply screaming at them nonstop. All it'll do is have them grow up thinking that's normal, hardly knowing how to be polite.

Another reason he likes being one of Giovanni's favorites is where he has a better chance picking where he wants to work.

He was completely ecstatic about working in Johto, working in one particular location to exact.

It was safely snugged in the middle of the wilderness, away from pesky people, trainer and civilian alike. It wasn't a nature reserve, so no worries of rangers and officers wandering through and discovering him.

And if he were to become too stressed and needed to step away from work, if the weather is favorable, he'll take a walk outside. He loves the fresh air, there's only so much chemicals and sterile equipment he can take before it drove him insane.

By walking, he can clear his head, relieve himself of any headaches present or threatening to come. It would give him time to think alone, giving his team a break as much as getting one from them.

It honestly helps, usually coming back with fresh ideas to continue or discover what the issue at hand is.

On the plus side, being so far out, practically owning the lab, he could make his own deadlines. He can calculate a rough estimate of how long it would take, then throw in an extra month or two as a precaution.

Gives himself and whatever team he gets plenty of time to get work done, or in this case, having multiple projects dropped in his lap nonstop.

Drawing himself out of his thoughts, he found himself a chair, laying claim to it before anyone else could.

Not entirely caring about posture, he attempted to relax, to fight the urge to get sick, ignoring any stares sent his way.

After a few minutes, he begrudgingly opened the file, mildly curious what it could be to have dragged him here in the first place.

"Wonderful…" he grumbled angrily, his already sour mood getting worse.

There was almost no information, most of it blacked out, just bits and pieces, namely who he needs to talk to. Regardless, it was enough to tell him it was a huge project with an already premade deadline.

He _really_ hates premade deadlines; he prefers to make his own…

If something screws up, he'll get blamed for incompetence, even if it was out of his hands to begin with.

Whoever this guy is better know what he's doing or he'll have hell to pay.

He'll _personally_ make sure of it…

A hand landing on his shoulder, Sebastian glanced up, seeing a friendly face, a far _too_ friendly face to belong in a place like here.

"You okay?" he asked, concern showing.

"No…" the other admitted knowing that lying would only get worse.

Didn't help that he already began to take a few deep breaths to fight back the urge to throw up, the smell of coffee having hit his senses.

If he didn't feel like shit right now, he'd take after that idiot who just walked passed them and probably strangle him.

Oh how he wished he could give Giovanni a piece of his mind…

"Jet lag I presume?"

"How'd you guess?"

Taking a seat, the Johto scientist could only guess that this new face is also a scientist, though wore a normal button up shirt and slacks. He would have worn something more casual himself, but with how urgent the message was made, he had no time to change out of his lab wear.

When taking in his facial features, seeing he wore glasses, had white hair and beard, the scientist figured he had to be a few years older than him.

"I've had my fair share," he answered with a reassuring laugh. "That and I came here a few days ago and felt the same way. Probably plotting to murder that guy who walked by us just now?"

Sebastian let out a small groan, hanging his head between his knees, feeling a hand rub his back, the gesture comforting.

He hasn't had someone treat him like a human being in a long time.

They're either too afraid of his antisocial nature or find him not worth helping.

Hearing something crinkling, he slowly sat back up, seeing the man holding out a couple of crackers.

They looked like the cheap ones from the cafeteria…

"Should help settle your stomach. Had swiped a few when I was feeling ill at the cafeteria, so help yourself," he answered with a smile.

"Or keep a kid from getting sick," the younger man half laughed, now grateful for the small treat.

"You got one?"

"Sort of…" Sebastian replied softly, eating so he wouldn't have to talk.

"I used to have a daughter," the older man replied solemnly.

"What's her name?"

"Amber."

As if on cue, he fished through his pockets again, pulling out his wallet, removing an old photo showing a little girl with beautiful blue hair.

"She's really adorable," Sebastian answered, mildly jealous he had a photo while all he has are memories.

Just looking at the photo, he knew it was far older than it should be, making him probably more curious than he should be. Yet, it didn't stop him from asking the other, silently praying it won't backfire.

"What happened to her?"

Why is he sounding so concerned for this man, a man he just met?

Sure, he's willing to be polite since the other is, having in a sense offered help with his jet lag no matter how measly it is.

"She had been born with a very serious illness. My wife and I didn't know it until she collapsed one day."

"Oh gods…" the normally cold scientist gasped, feeling a twinge in his chest.

"We tried to save her. I even began using my cloning research to try and recreate her damaged organs, make them healthy and disease free. But it wasn't enough, in the end, we still lost her."

"I…I'm so sorry…"

"I should apologize; I shouldn't have dropped it on you like that," the man spoke, giving him a sad look that strangely pained the younger man.

"It's quite alright. Having to hold all that pain in. It must've been almost unbearable," Sebastian whispered, trying to reassure the other.

"It really is… You know, you're the first person here to actually show some sympathy when asking about my personal life."

"I can only imagine the pain you went through. I have a couple of daughters of my own, we're _estranged_ from each other, but I still love them. I wouldn't know what I'd do if something like that happened to them."

"It's any parent's worst fear and it becomes their greatest nightmare."

He couldn't help but agree, feeling sick, but for a whole new reason as he stared at the tiled floor.

It was enough to make him stop munching on the crackers, knowing if he continued, he'd just get sick.

"What brought you here though? This isn't _exactly_ a good place to work while mourning," Sebastian asked, hoping he didn't sound too harsh.

Why is he still showing concern for this man?

This isn't the first time he's heard a similar story, parents losing their child, learning who was a widow, orphaned, the list going on.

What makes this man so special?

"Shortly after Amber's passing, I found out what was wrong with her. If I had found it sooner, I could've cured her…"

Still unsure what he meant, the Johto scientist looked at him, completely focused, ignoring any and all who walked by them.

Right now, it felt as if they were the only living things in this cold hallway.

"I _could_ bring her back, but my equipment wasn't enough. All I could do is preserve what little DNA I could salvage. I would've tried getting more, but at the time, in my wife and I's grief, we had her cremated. Any I have now, they were from old hairbrushes and baby teeth she began losing."

"Are…are you talking about _cloning_ her?"

"Yes, I can do it, I _know_ I can, but I needed money. All I had left was barely enough to support myself, my wife having left me. She thought I was mad and I couldn't bring myself to beg her to stay, to help me. She suffered enough as is, and I couldn't be angry at her for not having faith. If the roles were reversed, I probably would've left."

"So, Giovanni heard about you then?"

"More through a newspaper."

"Newspaper?"

Nodding, he gave the other a small smile, "I was in Sinnoh looking into new cloning options and attempt to get funding for research. While I was there, I heard about how a little boy lost his hearing, a madman using him in some sick study. I felt horrible for him, seeing how distraught his parents were when I visited. So I offered to clone his eardrums and have them surgically implanted."

"I'm surprised you _didn't_ get funding."

"It wasn't entirely a new thing over there, but I foolishly did it out of my own pockets when seeing how bad off they were financially. This of course set me back quite a bit, barely making enough to return home."

"I see…"

"When I got back to Kanto to compare notes and such I gathered, Giovanni called and asked to see me. I invited him over and surprisingly enough, he _actually_ swung by himself. You don't know how surprised I was to see a gym leader interested in my research, let alone want to fund it. So of course I jumped at the chance."

"That _is_ rather surprising…"

"All he asked in return was to create clones for him while I worked on bringing my daughter back."

Recalling the folder, the Johto scientist gave it a wary glance before returning his gaze back at the man.

"By any chance, is your name Dr. Thomas Fuji?"

"Y-yes, how did you know?"

"Apparently we're partners now."

He showed him the folder, seeing how his eyes lit up.

It was then he saw that the smile he got before, it was fake, disappearing almost entirely when talking about his daughter and his struggles. But the second he uttered those words, showed that folder, this smile, it wasn't fake. It was filled with joy, filled with hope. And strangely enough, he was happy to see it, that he's the one to bring about such an emotion.

"Then you're Professor Shiranui Sebastian? What are the chances we'd meet like this?" the older man laughed, earning a small smirk from the other.

"I _just_ arrived here. I guess if it wasn't for jet lag, we likely wouldn't have bumped into one another until called together."

"That may be true, but I'm glad to meet you. I actually know a bit about you."

"You do?"

"Yes, when I was made head for the cloning research, I knew if Giovanni wanted me to make clones or tinker with them, I'll need help. So I requested a list of all his best scientists that have dabbled in cloning, fossil revival, etc."

"I studied some, but I mostly specialize in evolution."

"I know, but out of all the others, I felt that you were the best, most reliable one. When I asked about you, Giovanni told me you're one of his best when it came to meeting deadlines and getting the job done."

"Has he told you _what_ I did?" Sebastian asked almost nervously.

"No, I forgot to ask," the other laughed, a light blush forming across his face.

 _"_ _Is he serious?"_ the younger man wondered before mentally shaking his head of the other's actions. "So, you wanted me to work with you on a cloning project?"

"Pretty much. Although we won't be working together directly I'm afraid."

"Hmm?"

"I guess I better start from the beginning," Fuji laughed nervously as the two got up, deciding to go someplace more private.

Finding an empty room, they sat down, bottles of water retrieved from a nearby vending machine, they began once more.

"Before I came here, I had been sent out with an exploration team into Guyana, to a shrine dedicated to Mew. But aside doing studies on it, there was something found that has led me here, the _two_ of us here to be precise."

"What _kind_ of find?"

"An eyelash of the very Pokémon the temple was built for."

"You're…you're joking."

"I'm not, but not only did we find an eyelash of a Mew, when the DNA was tested, we determined the sex had to have been male."

"But I thought all the males went extinct nearly a thousand years ago?"

"They have, the eyelash is badly corroded so it'll take much longer to extract enough to do what we need. Though we will have to make adjustments to fill in the gaps left behind due to the corrosion. It was a miracle it was as good as it was when it had been found."

"How are you sure though this _is_ indeed Mew?"

"It has to be, the way the DNA signature is written, it's completely different from all other Pokémon that exist. Either we have ourselves a Mew or we're about to clone an entirely new species of Pokémon. Either way, I'm sure that Giovanni would be excited at the idea."

Still shocked at what he just learned, he looked at his trembling hands, the scientist unsure how to take it.

What this man before him is claiming to have found, is planning to revive, it felt so surreal, as if he was in a dream.

And the fact _he_ was asked to work with him, he felt so honored…

"What _is_ my job exactly?"

He needs to know what his purpose here is, to know what he'll do, if it's actually worth it or should back out now.

"The eyelash found ended up not being the only one discovered," Fuji grinned, excitement threatening to burst free. "We found other samples. They're exactly the same save for being female."

"I'm guessing you want me to work with the other samples?"

"That's correct; my hands are going to be full with the male as is. I'm pretty much the only one who can repair it, know how to alter it safely without destroying it."

"What condition are the female samples though?"

"Sadly about the same, so before I let you work bringing them back, I'll be working on repairing them as well."

"Make sense…"

He couldn't believe it; he was being given such a heavy task, possibly his greatest, which in turn made him scared.

If he screwed this up somehow, whether by his hand or an act of the gods, he was a dead man.

"Aside cloning more Mew, what exactly _do_ you want me to do though? I know cloning in general is difficult, at the same time, it sounds rather simple for a man such as you," he nervously asked, swallowing a lump that began forming in his throat.

"I want to try something with the growth rate. With the male, I have to focus everything on its survival, so I can't risk doing anything new. If we had more than one, then I might've given it a shot. That's where _you_ come in. Since we have several samples of female Mew, we have more to tinker with."

"It makes sense when you put it that way."

"As we both know, cloning is still relatively new when it comes to recreating certain cells, be it organs or tissue. Even the technology is used for fossil restoration so long as there is stable DNA inside it. But what of the DNA that's not as stable or it had been contaminated such as my daughter's had been riddled with disease?"

"I think I get what you're saying. You want me to examine the growth patterns, by slowing it down? Look for key patterns, any potential anomalies that could pose a risk to their development? That way if there _are_ problems, we would be able to perfect it better for future cloning projects."

"That's exactly correct. From what I read and been told about you, you can spot things far better than most."

The younger man couldn't help but smirk, feeling a bit proud of his work taken so seriously, his dedication to perfection applauded.

"And your main study is perfect for another part of research that's been given."

"What is it?"

"You've heard of this unusual evolution in the Kalos region, correct?"

"A little, you want me to study it?"

"Yes, aside it being a given task, I'm rather curious about it."

"To be honest, I've been rather curious too, but it wasn't something I could simply request to work on. So if it's an order from Giovanni, then I'll take it."

Hearing the man speak, it was motivating, a huge boost to one's morale, he couldn't help _but_ agree.

He knew the man only did this to bring his child back, to help parents everywhere who suffered such a loss. They could have the option to bring that child back, and in some ways, he was happy about the idea too.

But he thought about whom his boss is, what Giovanni was capable of.

He would abuse this man's creation, creating monstrous weapons from ancient creatures, having them manipulated to his needs.

He felt bad about it, but knew if he backed out, this man won't find another who would understand him as he does.

They're fathers, both childless in some ways, one through death, the other having no clue _where_ his babies are.

The man is depressed, seeing past the smile he wears to ease others much like how he wears a cold mask to keep people away.

They were more alike than he would've thought.

* * *

 ** _Throughout the fic, you may have noticed some names that appeared in the anime, also different, namely those who had no known first name or unknown if its a first or last name._**

 ** _Therefore, I thought to do that, giving Dr. Fuji a first name to go by as well as one for Professor Sebastian. Course in his case, I merely took his Japanese name since it sounded cool._**

 ** _If you feel I should change the_** "names," ** _I'm open to suggestions, same with the chapter/story in general._**

 ** _As for the plane thing, got the idea mostly from my mom since she hates flying with a fiery passion. Sadly I never flew, so I'm only going based on what I hear or have seen in a show/movie._**

 ** _Other than that, please read and review_**


	2. Chapter 2

With the project in its infancy, both men had plenty of time to get to know one another as they waited.

When they had to focus on some work at headquarters, they would team up, usually if it related to their project.

Sebastian wanted to make sure that he knew what was to be done, the other willing to show him.

The younger man was in awe when he first saw the premade lab for the DNA samples to be repaired, watching the other work.

He almost felt like a kid in a new toy store, but unlike _most_ kids he kept his hands to himself, willing to watch the other work.

Anything he _did_ do in the lab was minimal.

He was a genius, no doubt about it, but there were areas even _he_ wasn't as talented in as he would have liked.

But his company seemed the world to Fuji, so he was content to sit, either make small talk or read as he waited.

As days turned to weeks and months, spending time together, both became close friends, nearly inseparable. They would often be found walking together, eating, even laughing and poking fun at one another.

Sometimes they would step out for drinks or go out and watch a movie, giving themselves fresh air. But most of the time, they stayed in the base; keeping close to their work to ensure nothing went wrong.

Many who knew the cold scientist were surprised just _how_ human he really was, that this new face brought this side out.

Both men knew it wouldn't last forever, once the DNA is repaired, have been stabilized, they would separate.

They would be sent to their own respective labs to work without interruption, isolated from many to avoid being caught.

Sebastian wasn't sure if he'll know where Fuji will work on his projects or if the man is allowed to tell him and vice versa.

But neither of them really despaired all that much, they were sure they would have plenty of times to meet still.

They would likely have to return here, to send in reports about the clones' progress, comparing notes with each other. They may even be given some new projects to work on outside the clones.

But between that, they could use the time before returning to their labs, to hang out and share things. Catch up on how the other is doing, learn any new things, maybe share a few funny stories that went on during their time apart.

It wouldn't be easy, but both were determined to make their newly made friendship work in this dreadful place.

"Shi!" Fuji called happily.

The older man had walked over, a lunch tray in possession, his smile resting on his face, enough to light a room.

Despite the sunny smile given, Sebastian still scowled at the nickname, the other teasing him not to pout. It didn't last, being replaced with a rather mischievous smirk, the older one still grinning like a goof.

"Hello to you too, Tommy."

His smirk only widened as his friend's smile turned into a pout of his own, something no grown man should be capable of. But it didn't last long, breaking out into his familiar smile, laughing as did he.

"You seem awfully happy," Sebastian chuckled as they ate.

"I finally finished putting together teams for our projects. You'll love your team, they'll be perfect," Fuji answered in between mouthfuls.

"Oh _really_?"

"Well, being that we're bringing life in the world, they'll be confused, scared even. They need people who'll treat them with compassion, to ease them into a new life. I wanted to make sure that who we get will fit those roles as well as know what they're doing to avoid any screw-ups."

"That _and_ we're dealing with psychic types."

"Exactly, my friend. They'll be more sensitive to emotions, which will make them more difficult if you have the wrong person handling them."

"Anything else I should know?"

"Yes, I found one of them is quite knowledgeable about evolution, even hailing from Kalos. So I'm sure he'll be of great use to you with that research as much as the clones' development."

"That's great, I appreciate it."

"No problem."

As they talked some more, a woman slowly made her way over, a cruel grin across her face.

Taking advantage with them so engrossed with their conversation, she startled them by speaking, leaning over the table.

While she had no visible cleavage showing, her shirt was tight enough to leave little for imagination.

"My, my, Shiranui, I never thought a cold bastard like you would be capable of making a friend. I'm quite surprised."

"Meiya…" the other growled softly, his cold mask reforming.

Seeing him act like this, Fuji couldn't help but frown a little, wondering what kind of history these two must have.

Turning back towards the beautiful woman, he tried to give her a friendly smile, even holding his hand out to her to shake.

He hoped that if he gave _some_ respect, maybe she'll act nicer as would the younger man, ending whatever issues they have.

"Hello, I don't think we ever met before. I'm Thomas Fuji," he greeted with his familiar smile.

However, the woman simply gave his outstretched hand a sneer, making him recoil it as if he had been bitten.

"I know who _you_ are," she responded, not all that interested in him.

"Is there a reason that _you're_ here?" Sebastian half growled, trying to keep his temper in check.

How dare she come by and ruin their conversation!

She even had the gall to toss aside Fuji's kindness like it was used tissue!

"Can't I say hello every once in a while?" the woman teased.

"Only when you have something to rub into my face," the other spat.

"Smart man."

"If it'll get you out of our faces, what is it?"

Appearing delighted to brag, she gave them a grin, "Oh it's really nothing. I just happened to have gotten a rather big promotion."

"Heh…who'd you have to blow to accomplish _that_?" Sebastian sneered, his smirk growing by how red her face became.

What he didn't expect, was how fast she slapped him across the face, the force being enough to knock his glasses to the ground.

"I'd watch what you say to your superior, you little worm!"

With that, she stormed off, the other still seated, obviously furious as he held his stinging cheek, gritting his teeth.

"Shi, what the hell happened?" Fuji asked with a light hiss.

He wasn't sure whether or not to be angry, just couldn't decide it was from his friend's rudeness or the woman's attitude.

"My ex-wife…" he growled, nursing his cheek.

Okay, that was _really_ stupid of him; he was just lucky she simply slapped him and didn't pull a gun or knife on him instead. She didn't even think about beating the living shit out of him.

"Ex-wife? Wait, then _she's_ the mother of your daughters?"

"Yeah, that cheating hussy is the mother of my girls!" he snapped, getting up to search for his glasses.

He was startled when they were placed into his hands, making him turn to Fuji's blurred face.

"Thanks…"

"Shi, come on now, just what _happened_ between you two?"

"She used me, that's all there is to it."

"You really cared about her, didn't you?" Fuji asked softly so only the other would hear than nosy people.

Gently, he placed a hand on his friend's shoulder, willing to hear him out.

After a bit of a pause, clearly unsure, or maybe still finding it hard to trust another, the Johto scientist finally surrendered.

Then again, he just couldn't find any good reason to _say_ no when that man made such a pitiful face.

How they even became friends is beyond him, but he isn't complaining.

It has been rather nice having someone to talk to, have someone care about you, want to know more about you and you know more about them.

"Fine, but could we go somewhere more private?"

"Sure thing."

Helping him to his feet, the two collected their trash, throwing it out, anything else pocketed if possible to eat later.

Both went to one of the vacant rooms, the younger man knowing it isn't wired, so they would be safe, _he_ would be safe telling.

Once they were settled, the other almost began to fidget, unsure how to begin, but seeing the reassuring smile, he started.

"I thought I did long ago. I was new, practically an intern fresh out of college, one of the youngest. You could even say I was a prodigy from all the diplomas and certificates I had earned. Yet despite how brilliant I am, I was still gullible enough to end up working here, meeting _her_."

"What about her though?"

"She was a new grunt brought in, a couple years older than myself. We met in the same team for a project. I instantly fell for her. She was beautiful, she was smart, had a laugh that could melt hearts. I was young and really stupid. I didn't see or refused to see past who she really was."

"Things like that happen though…"

"I know, but it still hurt far worse than you could imagine. When the time was right for _her_ , she flat out told me how she never loved me. She simply used me for her own entertainment, to avoid boredom. She thought I was a cute toy to play with, watching as I do anything for her."

Fuji could see the other's face turn a shade darker, head turned away in shame, clearly hurting at the memories.

Whatever she did to him, it must've been uncomfortable or possibly to humiliating to ever repeat with another.

"She married me more for her own amusement, seeing how far I'd go, seeing how happy I was being with her. She didn't marry me for my money. She didn't marry me for my research or any recognition. She did it solely out of boredom… That's what hurt me the most, that and when she became pregnant."

"Shi…" Fuji sighed, seeing how hurt the other was, starting to understand why he acted cold around so many save for himself

This woman, she abused his trust, crushing it into the dirt.

The man was right, the way she did it, _why_ she did it, it hurt far worse.

If she had done this for his money, he'd be angry and hurt, but he'd also heal.

Instead, she merely toyed with him, even willing to get pregnant so she could in a sense utterly destroy him.

She ruined his love life, and likely made him feel insecure about himself.

Then not only leaving, but wounded him further by taking away his daughters to Arceus-knows where.

It made him wonder though, the way he talked about himself, namely when he first joined this place…

"Shi, how old _were_ you when you graduated?"

"Fifteen, like I said, I was considered a prodigy…" he answered softly.

"And her? How old were you two when you met?"

"I was sixteen and she was eighteen."

He wondered if the other will turn against him, finding just how much of a dumb kid he was all those years ago.

"When I turned eighteen, I proposed to her and we married the next year, and a few months after that, she became pregnant."

 _"_ _Oh Arceus."_

Hearing this, it really broke his heart, seeing how much his friend had suffered for another's entertainment.

"I'm sorry, Thomas, but could we drop it, please?"

A little disheartened, he also could see how distraught he was.

His dear friend didn't want to deal with the painful memories any more than he may already.

He didn't want to recount when he lost custody of his daughters, lost them completely to that witch. May not want to think about whether they know him, if they love him or hate him.

But hearing how young he was, they _had_ to be close or are young adults by now, unsure how many times he got to see his girls.

Would he know them if they walked down the hallway or would they recognize him as their father?

No, he didn't want to be responsible pushing his friend over the edge.

So he did what he felt any friend should do…

"Sure thing," he answered, a comforting smile on his face. "Just know this; I'm always here for you. We're friends, we support one another."

Still unsure, having mostly spilled his guts out to a man he was still learning, he gave a hesitant smile.

"I will; thank you."

* * *

 _ **I apologize if Sebastian seems to OOC, but at the same time, he** is **a minor character, so who knows what kind of a person he** really **is, right?**_

 _ **I tried to at least work it, if anything more of** how **he became the way he is, and in a sense, how much he trusts Dr. Fuji to tell him something so personal. I hope I nailed it or was close enough to make sense.**_

 _ **Please read and review**_


	3. Chapter 3

Despite how awkward things became after the confrontation, the two were able to push past it, acting as if nothing happened.

However, just as things began to return to their normal routine, they were forced to change it again.

The clones were ready, carefully shipped to their new destinations, their respective scientist right behind them.

Sebastian was focused on his work, his mind forgetting the incident at the cafeteria, the clones being on his mind.

When he first arrived at his lab, he was astonished how well furnished it was, given equipment he never thought he'd get to see, let alone use.

The team that Fuji picked was indeed excellent both in credentials and their personalities when speaking with them.

They were friendly like their head researcher, but unlike him, weren't overly chatty, giving space when needed. It was like they were picked solely for him and no one else in the world.

At least one of them was a woman, Cassie being her name. He guessed that her placement was likely to help play a maternal role for when the clones are born.

It makes sense really, while a male _could_ fill such a role, a woman is far better suited, especially when going by instincts.

Women are at times more docile with children and baby Pokémon, so it's only natural that a child would turn to a female more than a male.

The rest of the researchers had their own specialty, some he was really pleased to hear as much as the woman's.

One specialized in DNA itself, Davin being his name. He would read the strands well enough to point out oddities or anomalies before and after the clones began to grow.

His talent made it easier and faster to do minor tweaking during the beginning stages of their development shortly before they were shipped off.

Sebastian actually recognized him, seeing him working with Fuji in the lab while repairing the DNA. So to get him as a member of the team, he felt oddly flattered.

He was also a devote researcher with the Mew species, so his knowledge would come in handy if needed when they're born.

Another of the researchers was named Joel, a name that seemed rather suitable to someone who had been born and raised in Kalos. It was him that he would work with when reading about the new evolution and take notes. Not only that, he specialized creating the synthetic embryotic fluid used to sustain the lives inside the tubes.

Cassie also specialized in the same field for the fluid, but also creating machines to mimic heartbeats and such. Therefore, they would be turning the test tubes almost into artificial wombs that they could see into.

That man though, Joel, he's exceptional in his main field of study. He's intelligent, very friendly, and a talented cook, his father apparently being a well-known chef in Kalos. Because of it, they often got treated to various recipes from the man's homeland than bland meals or nonstop takeout.

But his knowledge regarding this new evolution, one he called Mega Evolution was fascinating, drawing the other in.

He had been told that this young man had once studied under the infamous Augustine Sycamore, making him all the more valuable.

As for the rest, they were all recent graduates, but with excellent marks in the medical field, particularly cloning.

Fuji made sure that his team was well balanced, to support him for when he's stumped, knowing he had no worries about turning to them for help.

It also meant that if he had to leave, he could safely leave the lab in their charge, picking the one the rest respected and listened as much as they would listen to him.

He could only imagine what Fuji's team must be like, if they're like his or completely different.

Does he have more people because of the multiple projects compared to him?

Wouldn't surprise him if he did, he was told before they separated not only was he cloning the Mew and his daughter, but the Kanto starters too.

That alone showed he had way more on his plate, course so does he when he thinks about it.

Not only does he have this project to work on, he still had to work on his other projects, having neglected them enough.

He was just glad that he _had_ been picked for this, even agreed to participate, at least he has a _partial_ excuse for some running late.

Once his other projects were done, he found himself becoming further engrossed monitoring the clones.

They were tiny right now, barely any form and shape to determine what they'll look like, but he was sure they would be amazing as they get bigger.

Before they were due to leave, Fuji gave him several notebooks to write down their progress as well as personal thoughts.

They even came up with names to give these creatures, more so by how much alteration they had to do to ensure the clones would live.

Mewtwo…

A fitting name really, they are clones, yet it sounded powerful, _knowing_ they would be powerful.

He wouldn't be all that surprised if they end up stronger than the originals, where someone may confuse them _as_ originals, not the other way around.

Both were determined to ensure they came out healthy; they came out powerful, that whatever killed them in the past wouldn't repeat so easily.

Not only were they going to be blessed with a new name, but have a secondary name to go with it.

They decided to use the term Alpha for the male, being he had been found first, and likely would be _born_ first if all goes well.

It'd be a fitting name, a strong name if they decided to actually name him that than call him by his new species' name.

The two he's working with, the clone on the left would be Beta, being the second sample found, the other called Omega, having been the third found.

While there were other samples, they're currently on ice, safely protected from thieves and decay. These samples were stored back in headquarters where they would be safest from such things.

They were completely unknown, but assumed to be more of the species they're working on due to being found within the vicinity of the ruins.

As for whether they're all female, they weren't sure, not wanting to mess with them more than they had already.

The months that passed by, Sebastian found it moving by to quickly despite how slow the clones grew.

As Sebastian walked in, greeting his team, gaining fondness of them, before focusing his attention the twins.

He carried his notepad and a pen pulled from his pocket to take some notes down.

"To think we _all_ in a sense looked like that when first conceived," Davin stated with a small laugh.

He had taken specially prepared cleaning supplies to wipe off any dust and potential grime off the tubes.

"It really _is_ amazing how small and helpless we looked in our mothers' wombs," Sebastian replied as he finished taking notes.

Walking away, he put them in his own assigned locker, stretching his arms to let the joints pop back into place.

"What color do you think they'll be?" the other asked.

"Who knows, they could retain the original color or come out entirely different."

At this point, he was focused on another matter, remaining attentive in case he was asked something or the other decided to continue conversation.

He was already pulling out several books, Joel coming over, both reading various books regarding Mega Evolution.

Many of these books the lab assistant had brought from home, some having been signed by the very people who wrote them.

"I'm sort of hoping they'll be a different color. It'd give them more individuality as a new species," Davin laughed as he finished, walking off to put things away.

"Very true," he spoke, reading the books, taking notes in another book.

It was like this for a while, something he was pleased with, though when he got called back to headquarters, it wasn't as pleasant as he would have liked.

When he and Fuji arrived to hand in their reports, they also ended up having to help with restoration on various data.

Apparently someone not only broke in and stole most of the samples collected, particularly the ones Fuji found at the temple, but hacked into their computers as well.

Not only were samples stolen, but the data Fuji put together in order to restore and successfully clone them were as well.

Whoever stole them were talented, not even the best of Giovanni's own men able to find out who or where they may have gone.

At first, it was suspected that one of them or one of their team members was responsible, but after investigating, were all cleared.

Once the dust began to settle, both men took some time to catch their breath and take advantage of the time they have to hang out. It would be a few days, a week at most before they're due to return to their respective labs.

During this, Fuji had taken Sebastian out for drinks, even dragging along several others he managed to make friends with.

How he managed it was beyond him, but dared not ask, he seemed to have this spell to captivate most people. He just had this _magnetic_ personality, attracting people much like how he had been.

It was also obvious he wanted the younger man to socialize more, not wanting him stuck with only one friend, possibly his research team, while pushing others away.

And by some magic, it began to work, sure Sebastian didn't like _all_ the people Fuji brought, he at least got along with a few, one of them named Tyson.

They were somewhat similar personality wise, albeit he was more social, having seen him joke with others time to time.

He was also intelligent, meaning if the two started going into more scientific conversations, he'd actually _have_ something constructive to say.

He didn't have to pretend to be smart, and if there was something he didn't know, he would let them know in some manner. He wasn't embarrassed about asking; something the scientist couldn't help but feel a little envy for.

Tyson was also a bit of a ladies man; not that either could blame him; he was much younger or appeared to be. So it wouldn't be a surprise he'd be popular with the ladies, as for whether he actually _slept_ with them or not, they dared not ask.

The only thing Sebastian found a tad annoying were some of the man's bad jokes, although Fuji somehow thought they were hilarious.

Sometimes the older man would tease him about how he should ask Tyson for some dating advice. The younger man would of course retaliate about how he should too being he's single as well.

They were comfortable with each other to say such things, knowing if another were to make that joke, it would hurt. But with each other, it was friendly and comforting, no malice behind their words.

They were simply content spending time together when they can, going out for drinks, watching a movie or two at a hotel or theater. It could be just the two of them or a handful of others they could tolerate, the younger one mostly.

Soon enough, their innocent fun had to end, returning to work until the next time they're called back.

As Sebastian returned, he shared what happened with his team, the others worried, but grateful he and Fuji defended them all.

And like that, they continued on, at some point, Sebastian given another project to capture the legendary beast, Raikou.

Being this was a legendary Pokémon, he had to study what he could about it, know what the best solution would be. From there, find what sort of cage, tank, whatever they need would work best.

While a Pokéball could work just as effectively, it was also something they couldn't waste time on. With what it can do, battling was almost impossible without proper resources to trace its patterns to properly trap it.

But it wasn't just that, the power it possesses was immense, chances of actually _beating_ a legendary Pokémon was slim.

Therefore, he worked tirelessly on this project, sending people out, giving orders on collecting samples or obtaining books regarding Raikou.

During all this, he would take small breaks, checking on the clones and his team, finding a sense of pride as they slowly grew bigger.

But he also found himself beginning to feel this protectiveness over them as well, knowing he can't get attached. If he did, he may not have the strength to let them go once they're born, let Giovanni take them.

He knew that his team was getting attached too, seeing how they fondly stared at them, chatting or giggling how cute they were going to look as they got bigger.

The man wanted to scold them, snap at them that they're scientists, not soon to be parents, but it constantly got lodged in his throat.

He wanted to stop it, not because they _were_ scientists, but go through the pain he's gone through once. He didn't want them to go through that pain of having something precious taken away.

Within months, almost a year, he nearly completed his latest project before called back to headquarters to send in his report about it and the clones.

Upon his arrival, he later found Fuji, though his normally chipper demeanor was gone, almost wiped clean.

Seeing that unnerved the man, knowing _something_ was wrong, knowing _he_ had to find out what's wrong.

Fuji promised to be there for him, so it's only fair to do the same for him, for the man he considered a friend.

After sending in their reports, taking a few days to themselves before returning, for once Sebastian dragged the other out.

He took him to a bar, sitting themselves in a more isolated booth to give themselves privacy. The music was loud, enough to drown most of their voices from eavesdroppers, but not enough to not hear each other.

Once alone, drinks in hand, the younger man surprised when the other had asked for their strongest liquor.

Now he knew something was wrong…

"Thomas, what's wrong?" Sebastian asked, his face filled with concern.

Hesitantly, he placed a hand on the older man's shoulder, seeing him physically flinch, a choked sob escaping.

He prayed that whatever left his friend in this state, it wasn't serious.

As morbid as it'd sound, he'd be content to learn the starters died, or even Project Alpha regardless of the importance.

Just so long as…

"Mewtwo's all that's left," he answered, another soft sob escaping.

Sebastian felt his blood run cold at those words, watching as the man buried his face into his arms, sobbing heavily now.

"Wh-what happened?" he stuttered, still shocked by what he heard.

"I don't know, Shi, I just don't know. Everything was perfect; there was no disease, no impurities in the fluid, nothing. And yet, _something_ happened. Something killed not just Amber, but the other clones too. We almost lost Mewtwo, we barely managed to save him. I have no idea what will happen now. I don't know if he might have brain damage _after_ what happened."

"What happened to him?"

"His brainwaves were off the charts, we thought he was unconscious, maybe dreaming. We could only assume that he must've kept some sort of telepathic connection with Amber and the clones. He must've sensed their passing and became distressed. We had to inject a serum to suppress those emotions, erase the memories if there were any. I feel horrible doing that to him. He's so little, so fragile to go through that."

"Shit…" the other cursed, clenching his eyes shut, feeling so helpless. That is until a thought came to him, realization dawning on him. "We're not done yet, Tommy, we can still bring Amber back!"

He had to bring the man back to his old self, to know not all is lost, that there's still some hope left.

Not only did Fuji have more samples of Amber's DNA at the island, but he had given some to Sebastian as well.

"I know, but I don't know if I can try again. I failed so many times to bring her back, I don't know if I can ever succeed."

"Of course you will! You're her father, you love her and I know she loves you! If she's anything like you, she would _want_ to come back, to be back with her family."

Sebastian tried to hold his tears back, to try and be strong for the other man, but between the news and the alcohol, he found himself crying too. He wasn't bawling like the other had been, but enough tears flowed to show his pain.

He gripped the other man's hand, unable to let go, afraid if he did so, he would lose his friend, his only friend.

Looking at him, Fuji felt a small smile form, realizing that he was right about what he said.

Unconsciously, he reached out with his free hand, wiping the tears from the younger man's eyes, careful of his glasses.

"Thank you, Shi. I honestly don't know what I would do without you," he chuckled softly as he pulled the other close, hugging him tightly.

Unsure if it was the alcohol doing this, but Sebastian felt himself relax, smiling in return as he hugged back.

He never felt so comfortable around another person, not since Meiya tricked him, damn near destroyed his trust in others.

Pulling away, both starting to feel a bit better, the older one gave him almost a shy look, something the other found oddly cute.

"How are Beta and Omega doing?"

Taken off guard a little by the question, realizing how much he stared at the other, he felt his face heat up as he sipped his drink.

"They're doing really well, no exceptional," he answered with a sheepish grin forming. "Beta though gave us a _tiny_ scare."

"What happened?"

"We thought something happened as she somehow got bigger than Omega, not by much though. It appears to have been a natural occurrence, so we were relieved of that."

"I see, that can happen sometimes," the other chuckled dryly.

"To be honest, I never watched a fetus grow, not like this. The only ones I ever got to see were in jars from universities. It's so strange seeing them get bigger, regardless of how slow it is."

Appearing more relaxed than before, Fuji gave his friend his familiar smile, the one that made the other feel relaxed as well.

"Shi, if things turn out perfect with them, could you…"

"I'll do what I can to bring her back using this method."

"Thank you, you're a true friend."

"You'd do the same for me."

Feeling much better, the older man wrapped an arm around him, his cheeriness returning more and more.

"If that's the case, then drinks are on me!"

The younger man couldn't help but laugh, knowing that this _wasn't_ the alcohol talking. His friend was back.

Not wanting to ruin the mood, he joined his friend, allowing himself to let go a bit more and drink more freely.

They had a couple of weeks before they had to return, so a night or two like this shouldn't hurt.

* * *

 ** _Tried to fit the time sequence between following the anime's chronological order and estimate how long the cloning process likely would have taken._**

 ** _No matter how fast cells grow, it_** _would_ ** _take a while, especially with something like what they were doing with Mewtwo, right?_**

 ** _Please read and review_**


	4. Chapter 4

Sebastian groaned, wondering what happened, blurred eyes scanning what appeared to be an unfamiliar room.

The last thing he recalled was having drinks with Fuji, a few nights since they spoke and made the promise to bring Amber back.

But he couldn't remember _what_ they did at the bar, or which bar, the two sometimes going to different ones to change things up.

Normally he would've chalked it up to Fuji talking him into drinking _way_ more than either really should. It hasn't been the first time, and surely won't be the last, he's sure of that despite how many times he tells himself.

Whenever they get hammered, by morning and most of the day if not two days, they'd feel like crap. And when they do, they'll try sleeping it off at their hotel rooms or at their base in a spare room. It depends on where they go and which place is closer.

Whether this annoyed or downright pissed Giovanni off having two of his scientists act like college kids, he didn't care.

What he _did_ care was figuring where the hell he was, where Fuji was, knowing he wouldn't dump him in some unknown room.

If either were too wasted, they would mostly end up crashing in the same room, one in bed, the other passed out on the sofa.

Slowly getting up, trying not to move to fast, the room spinning enough as is, he didn't need to make it worse.

However, just as he sat up, he winced as a sharp pain went through him, an unfamiliar pain that now had him more awake and feeling terrified.

He located the source when he tried moving again, making his heart race faster than it should, his breathing quickening.

His entire lower half ached and stung, as if repeatedly beaten, but it wasn't just the pain that was making him fearful. He also felt sticky, the smell of blood filling his senses, blood, and…and the smell of sex.

Somehow locating his cracked glasses hidden on the pillows, he threw them on as he ripped the sheets off, a hand slapping over his mouth.

He was covered in various bruises, mostly around his thighs and wrists, signs he had been bitten and scratched.

He hardly had to move to know there was semen and blood near where he had been violated, the knowledge alone making him sick.

Unable to hold it back, he hung his head over the side, vomiting hard, tears starting to flow down his face.

"Oh Arceus no…" he groaned, having emptied his stomach.

What happened to him? How did this happen? Where was Fuji?

"T-Tom," he cried softly, curling up into a tight ball.

He felt so weak and helpless; all he wanted was for it to be a nightmare, a horrible, horrible nightmare.

At some point, unsure if it was minutes or hours, he began to hear frantic rapping on the door, the man freezing up instantly.

He was terrified to move to see who was there, so many thoughts running through his head; he started to feel sick again.

What if it's his attacker or whoever owned this room?

But why knock than barge right in?

Unless its maintenance coming to clean the room, unware of what transpired, the poor scientist unsure _what_ transpired himself.

Or worse, it _is_ his attacker, but he's taunting him before coming in to do who knows what.

Before he could stop himself, tears began to fall, curling up into a tighter ball, everything he learned slipping from his mind.

All that was in his mind now was surviving, was for his friend to come save him, to wake him from this nightmare.

"Shi!"

He recognized that voice, bloodshot and bruising eyes widening as he heard the door get kicked down, turning to face him.

"Thomas?"

"Oh Arceus," he gasped, covering his mouth in absolute horror.

On the bed, slowly uncurling his battered form, was his best friend, seeing how horrible he looked.

The pale skin speckled with black and blue marks, cuts from what appeared to be nails and maybe teeth decorated some parts. This was _no_ attack from a Pokémon, the sight, even the sickening smell enough to confirm what did this.

Despite being frozen at the door, the older man forced his legs to cooperate, hurrying to the other's side.

Ignoring the sticky sheets, he sat down, pulling him close, letting him lean into his body, feeling him trembling with choked sobs.

Fuji had never thought he could see his friend look so vulnerable, never _wanted_ to see him like this to begin with.

"Oh Shi, I'm so sorry!" he cried, rubbing the other's back. "I'm so sorry, I shouldn't have let try going back to your hotel alone. I should've made you stay, made _myself_ go with you. This is all my fault!"

Hearing him blaming himself, the younger man looked up, a few hiccups escaping as he struggled to compose himself.

"Y-you're here now," he sniffed, trying to give him a reassuring smile that he didn't hate him.

Resting his face against the other, he felt his pounding heart beginning to calm, the other's body heat providing comfortable warmth to his shivering form.

He didn't hate Fuji, he could _never_ hate him. It wasn't like he planned for him to end up like this. Neither of them did.

"Come on, we need to get you to a hospital. We need to call the police…" he started before the other recoiled suddenly, face filled with absolute terror. "Shi?"

"No! No police! We _can't_ risk being found out we're part of Team Rocket. We simply can't take the risk!"

"Dammit, Shi, you were raped! What are we _supposed_ to do?"

"J-just forget about it," Sebastian half whimpered, wrapping his arms around his shivering form, a defeated look on his face. "They won't care I was raped. Giovanni won't care either. No one will care…"

"But _I_ care about what happened! What if you get sick? I'll never forgive myself if you contracted something!"

Despite his words, whether they were convincing or not, the other had that familiar determined look. It was the same one he wore, that near begging, yet icy look he wore when asking him to drop the subject about his ex-wife.

It hurt him; it _seriously_ hurt him to see how just how terrified his friend was.

It made sense why he made this face. He didn't do it because he was embarrassed or being stubborn. No, he was absolutely terrified without actually admitting it.

It reminded him of that day when Giovanni nearly accused them for stealing the research on the Mewtwo project.

Despite how calm Sebastian looked, when they finally got out, the other couldn't stop shaking. Anyone who noticed, any who wasn't a friend, he would shoot that same look, shutting them up.

Fuji then remembered that this was a crime organization…

If Giovanni found out, he may determine his dearest friend incompetent and throw him away.

That man, without showing it, he _knew_ he was capable of killing someone, either by his own hands, a Pokémon, or hiring another.

The thought alone scared him, not wanting to imagine finding or read about his friend lying dead in a gutter.

And for what? To keep him quiet about what they're doing?

He nearly jumped when hearing his friend talk, hearing how cold, how numb he sounded, breaking his heart.

"I'll remember who did this to me. Once I do…once I do I'll have someone sent and make them pay. It'll be fixed, nothing to worry about anymore."

Despite how he sounded, he still looked so scared and vulnerable, shivering still, knees drawn up, chin resting on top.

"Shi…"

This is what the man is being reduced to, having to shove his emotions away, to avoid getting close, leaving himself open.

It made him wonder just how many others are like him, men and women alike who were abused in some manner.

How many are forced to deal with it like this? How many are unable to get proper help because of this organization?

How many are having to attempt to forget about it, ignore it, pretend that it never happened in the first place?

How many are wracked with nightmares, ones he's sure Sebastian will endure?

He needed to think of something to get him out of this line of work; he can't risk losing his friend to this place.

He can risk _himself_ becoming lost, become cold and callous as so many others have become.

If he did, he may push his friend away when he needs it, or worse, stop loving his daughter, treating her revival as another project. The thought alone terrified him far worse than the possibility of death, being imprisoned even.

Tentatively, he continued to rub the other's back, swallowing a hard lump in his throat to speak.

"Let's get you cleaned up and dressed. We can't stay here. If whoever attacked you comes back and has a Pokémon, a gun even…"

"I know…"

Slowly, they got up, the smaller man leaning, almost carried into the adjacent bathroom, the older man turning on the shower.

Leaning against the tiled wall, Sebastian whimpered as the cold droplets pelted his battered frame, slowly heating up into a more comfortable temperature.

He could barely move, barely support his weak body, so washing himself was out of the question. He had to swallow his pride and let Fuji wash him, unable to suppress a few whimpers escaping whenever a particularly sore spot was rubbed.

The older man felt sick as he wiped the blood and semen off his friend's thighs, washing the evidence away like it's nothing.

But hearing him make those cries, obviously in pain, still petrified, it broke his heart into thousands of pieces.

With as much cleaned off as possible, Fuji grabbed a towel, wrapping it around the other, drying him off.

Looking into those frightened eyes, he couldn't help but lean his forehead against his, the other relaxing at the gentle ministrations.

 _"_ _You're going to be okay. I'll make sure you never get hurt like this again,"_ he silently promised.

He guided the other back to the room, letting him sit down on possibly the only dry part of the bed so he could dress.

Searching the room, he managed to find some of Sebastian's clothes, though his shirt had been torn almost to shreds. The others were in just as bad a shape, where he couldn't leave without someone asking or appearing like a drifter.

Thinking for a bit, he got an idea, taking his coat off, setting it down, knowing that if his friend wore it, not only would he stay warm, but it'd cover him up nicely.

No one would see the tears and stains. He would even loan his scarf so he could burrow in it, hiding his bruised face.

He would be cold, but his friend needed the warmth more, needed to feel secure, so it would be worth it.

Slowly, he helped him dress, knowing perfectly well that while he could walk, albeit sluggishly, he was in no condition to bend over.

Whoever kidnapped him, they did a number and by how fresh the stains looked, it happened more than once, leaving him sore and stiff.

In a strange and sad way, it reminded him of when he'd dress Amber, before she became too sick to even leave the bed.

Once done, after much begging, almost pleading from the younger man, he collected the soiled linen.

Maybe there's hope that his friend _will_ get help?

Maybe they could find out themselves who did this and anonymously send it to the police to get justice.

Bearing that bit of hope, he took what he could to carry the linen, making sure the blood didn't show.

It made him sick, more so when he washed his hands, knowing he may never feel clean again after this.

No, touching those disgusting sheets would _never_ compare to how Sebastian must be feeling. He had been violated repeatedly, beaten, whether he fought back or simply for kicks, so may never feel clean again.

The thought depressed the older man as they went out into the cool night air, grateful it was late. There were less chances of running into people, good and bad alike, allowing them plenty of time to locate a bus stop and wait.

As they sat down, Fuji felt the other unconsciously burrow his face into his shoulder; his body not once stopped shivering.

He couldn't blame him really, aside the air being cold, but he was physically assaulted, battered even. He was lucky to be alive after that, to have been found before the sick monster who did this could return.

Fuji wasn't sure how he'd react if the same thing happened to him instead, if he'd be like this or worse.

Something told him that if it _had_ been him, he would be worse off than his friend is emotionally. He wouldn't have been able to think clearly, having not worked for this organization enough to know the risks.

"H-how did you find me?" Sebastian asked after a few minutes passed.

He had tried to sit up straighter, trying to carry more dignity, but it hurt so much that he couldn't help but squirm on the cold hard bench.

Before he knew it, he found himself wanting to burrow back into Fuji's arms, to get that warmth back. The coat and scarf just weren't enough to make him feel safe.

Just as he thought he would break again, an arm wrapped around him, settling him as he leaned his head into the other's shoulder.

He felt like such a child, knowing if anyone else saw him like this, he would be a laughing stock and likely a target for all to pick on. But with Fuji, he was safe, knowing he wouldn't hurt him for laughs, toss him aside like Meiya had done.

"I came back to see how you were doing, make sure you didn't pass out on the floor like last time. But you weren't there and it felt like a knife went into my stomach."

"So you searched for me?"

"Yeah, I don't know why, but I couldn't bring myself to get help. I guess in some ways, what you said, I knew it in the back of my head too. We're _both_ part of Team Rocket, if we're found out, we're screwed. But…"

"But what?"

"I've been searching for you for _two_ days. I was scared that the longer I took to find you, the less likely I'd _ever_ find you. I didn't want to think like that, that I should've thought more logically about it, but I couldn't focus. I couldn't risk losing you, never seeing you again."

"Thomas…"

"When I got to the seedier hotels, I knew asking about where you might've been wouldn't have helped me. Anyone I asked, they could've lied to make a quick buck, or lure me somewhere to rob me or kill me if they're connected to your disappearance. I regretted never having a Pokémon that could've searched for you, following your scent."

"So you started shouting my name? Praying that I'd somehow respond?"

"Not the smartest thing now that I think about it."

"Yet in the end, you found me…"

"I did, and I'm glad I searched for you, regardless how foolish it was to do it on my own. You don't know how relieved I am to know you're still alive."

"Thank you…" Sebastian whispered softly, a small smile forming. "Thank you for searching for me. For not giving up, not abandoning me."

"I'd never abandon you," Fuji stated, hugging the other as tightly as he could without hurting him. "I just wish I found you sooner, _before_ you were hurt."

Once the bus arrived and they were back at the hotel, the young man practically pleaded with him to let him change into something new.

Fuji couldn't blame him, wearing clothes that smelled like another, even letting him wash up a second time, this time able to sit down and soak in a tub.

He set aside spare clothes, seeing he was starting to move better, meaning he could dress himself, and if he couldn't would call for him.

What he didn't expect was later in the night finding him _and_ all the soiled linen and clothes gone.

Fearing the worst, he rushed outside, finding him behind an abandoned store, a fire burning inside a trashcan.

Without having to look or ask, he knew what was in it, seeing the other shivering as he rubbed his arms, refusing to stand close to the trashcan.

"Hey," he called, wrapping an arm around the other, feeling him flinch, making him frown. "Let's get you inside where it's warm."

Giving the trashcan one last look, he nodded, the older man guiding him away, letting the flames burn what evidence they could've used into ash.

"Shi, if things get too much, just know you can tell me anything. I don't care if its nightmares, related to what happened or not. I can't stand to see you try and bury your emotions like this."

"You said that before."

"And I meant it; I'll always mean it, no matter what."

"Even if I do, we won't be together for long…"

"I'll get us a couple of Pokégears, those new X Transceivers even then so we _can_ talk whenever we feel like it. I'm sure I can convince Giovanni to let us. They'll just be for us, no one else. We can use them for work _and_ personal use."

Before he could stop himself, Sebastian hugged his friend, arms wrapped around his shoulder, softly crying into him.

"Thank you," he whispered, calming down after a few minutes. "Thank you so much. I don't know what I'd ever do without you, if I never met you."

Recalling saying a similar thing, he hugged back, gently patting his back as he continued to cry for a little longer.

"Of course," he smiled bitterly, helping his friend into the bed, taking the couch for himself.

It was going to be hell for Sebastian…

The nightmares, the insecurities, and of course, Fuji would damn himself if he didn't get him tested.

How they'd accomplish it he wasn't sure, but he'll find a way…

Just before they arrived back at base to take care of some paperwork and run some trials on a few things they worked on, Fuji made a pit stop.

He bought some cheap concealer, getting it as close to Sebastian's skin color, to help him cover the bruises.

The fewer questions asked, the safer they are, the safer the younger man is. They would use it until the bruises healed. It wasn't perfect, but it had to do.

When they arrived, the older man still wracking his brain to get his friend checked out, keeping the younger man close.

If anyone asks why they're together more than normal, they'll claim they're discussing something relating to the project. No one would think twice about it, and hopefully won't notice just how off the younger man is.

Both nearly jumped out their skins when a hand landed on the younger man's shoulder, having him cry out, swinging a fist into the other's face.

Fuji tried to stop him, stop the other when he caught the fist, making the other briefly flashback to the rape.

"No! Let go of me! Let go!" Sebastian screamed, struggling to break free, surprising the other as he did so.

"Shit, I didn't mean to scare you two," Tyson apologized quickly. He backed away a bit as the smaller man crumbled to his knees, shaking horribly. "What the hell happened to you, Shiranui?"

Several of the grunts walking by had paused, seeing the shaken scientist, the other fussing over him. Some were concerned over the sight, others amused, very few continuing on with their business.

Knowing that he may not get answers with an audience, higher ranked Rocket snarled at them to get a move on. That alone sent the skittish grunts running, leaving them alone in the hallway.

"Follow me."

He glanced back while taking them to a separate room to talk privately, taking note how the smaller male limped a little.

He had a bad feeling about what might be told, but held his tongue than calling them out, not wanting to jump to conclusions.

The three alone in the room together, he glanced between them while passing a couple of water bottles to them.

"What the hell happened out there?" he asked, seeing the two flinch, obviously not wanting to talk about it. "Don't try to pretend! Tell me what the fuck happened now!"

He mentally flinched when the smaller one jumped, his normally stoic face crumbling away.

It was so unlike him, usually keeping his cool, even when stressed or panicked, an icy mask worn to keep others from pestering.

Very few knew what he was really like, but to see it break so easily…

"I…I was raped," Sebastian answered, the brunette shocked.

Did he just say what he thinks he said?

He didn't want to believe it, but the evidence was there.

Already the makeup started smearing off, revealing bruised skin, noticing how one eye seemed a tad more swollen than the other.

"How did this happen?"

"I don't know…"

"What did I just…" he started before shot a look by the other man.

"He's telling the truth, he honestly _doesn't_ remember. I found him last night, he was an absolute mess."

"Shit… What about his clothes? Where did it happen?"

"It was some seedy hotel downtown," Fuji answered, telling him how he came to find him, the other angry he didn't contact him.

At least until he was told _why_ they said nothing, weren't doing anything.

He couldn't blame them; blame Sebastian wanting to forget it, not do anything to get himself help. He _couldn't_ get help without it biting him in the ass.

Even if he got justice for the rape, he would only wind up in prison because of his involvement with Team Rocket.

And that's not counting what Giovanni would do if he found out about this.

He would likely consider him useless, more so if he doesn't get a hold of himself and shove the whole thing away. Their boss would simply hire someone to take the smaller male out, a _precaution_ to avoid him spilling the beans.

But like Fuji, he wasn't going to let the other off the hook to easily…

"Alright, you're going to get examined though. I'll get it set up to avoid suspicion. We'll just claim you were working and one of the newbies caused something to break and you got cut. Don't know what it is, so to stay safe, you'll get looked at to avoid a risk of it being contagious or whatever. You'll just wear some bandages on your hand or arm."

"Who's going to take the blame for this?" Fuji asked, wondering whose life is going to end for this lie.

"No one, in the chaos, name wasn't gotten. It'd be labeled as a freak accident, everyone gets a scolding and that's that."

"And to keep whoever tests me from saying anything?"

"You leave that to me."

* * *

 _ **This wasn't easy to write, not just the whole scenario, but** how **it could be pulled off without going way off course.**_

 _ **So I had to think,** "What would a member of an infamous crime organization do if forced into a situation like this?"_

 _ **Any skittish or easy to panic like Jesse and James, or possible newbie to Team Rocket, likely would run to the police, but because they're somewhat** "pathetic," **they might escape imprisonment. No hate please, I love Jesse and James a ton, but even** I **have to admit they can get pretty pathetic at times.**_

 _ **But with someone like Professor Sebastian, he likely wouldn't get so lucky, despite being a victim, he's also a criminal. After charges are filed and if/when his attacker(s) are caught and tried, he'll find himself arrested.**_

 _ **Then there's Giovanni. He wants a strong organization, and while some could probably get away with leaving or being arrested with no worries of information being leaked, those of a higher rank likely wouldn't be so lucky. If there was a chance they could leak information, intentional or not, he wouldn't want to take it and have them either forced to continue working or have them taken out permanently.**_

 _ **Hopefully I made it make some sense.**_

 _ **Please read and review**_


	5. Chapter 5

Just like that, Tyson kept to his word, Sebastian getting safely tested without anyone finding out the truth. And to make things better, all the tests came back negative, reliving them greatly.

Yet, he still felt horrible, feeling filthy, the feeling only going away when Fuji was nearby, calming him down.

Though when they got the Pokégears, again with Tyson's help to get the best and making sure no one would listen in, it made things _a little_ better.

The reception wasn't great, but it was better than nothing, Sebastian talking to his dear friend whenever he was free.

He'd go outside, finding a decent spot to talk with him with little trouble, calling him in hopes of him picking up.

Sometimes he'd call on planned hours, other times he'd be frantic, having had nightmares of the assault.

Two years of this passed, the older man wishing to help more, the younger one grateful for the help he _is_ getting just talking with someone.

However, Sebastian began to feel strange around the man, either standing with him or when they talk on the phone, their conversations more personal.

It was only after a particular dream he knew why he felt so odd now around his best friend…

He was in love.

Somehow, fell madly in love with his best friend, the _only_ friend he's ever made in this organization.

He honestly thought he forgot how to love since Meiya, the closest being his love for his daughters.

He felt happy, but was scared because of it too.

How would Fuji react if he told him?

Would he reciprocate his feelings?

Would he reject him? And if so, do it gently or find him disgusting and shove him away, never speaking to him again?

Those thoughts terrified him, knowing it was uncommon for two people of the same sex to be in an open relationship.

It was almost taboo, unsure how others would react if they did pursue such a relationship, if they _did_ end up together.

So many awful thoughts plagued his mind far more than the nightmares.

He couldn't tell Fuji how he felt, that was the last thing he'd ever do.

He didn't want their friendship ruined, the time they spent destroyed.

It tore him up so much, he loved the man so much, wanting to share that love with him, wanting to spend the rest of his life with him.

He admired the man, admiring his kindness with him and to others, regardless who they are. He was willing to be friendly to his ex-wife before learning the kind of monster she really is. He made friends so easily because of his kind nature, bringing out the better sides in people.

He admired his determination, how he won't give up and when he's close to doing so, something pushes him onward.

He was far more courageous, willing to speak his mind more openly about things, namely when it came to arguing with Giovanni when it came to the clones.

As he thought more about Fuji, Sebastian felt his face heat up, burying his head into his bedding as deep as it'd go, not caring if he suffocated.

Why did he have to be so handsome?

Have surprisingly strong arms, such a warm body whenever they _would_ hug?

Why did he have to be so affectionate anyway?

Why? Why? Why?

He could easily pick out all the little features the man had.

He could point out the few wrinkles that were on his face and hands.

He could easily spot the tiniest strands of color that remained in his hair.

He knew his favorite colors, favorite foods, what he didn't like.

He knew the prescription for his glasses, blood type, birthdate…

Oh Arceus, he wasn't just in love, he was obsessed!

Sebastian let out a frustrated groan, unable to get the man out of his mind, his dreams not helping.

While it was far more pleasant than his nightmares of that _night_ , he wished it was something _less_ arousing.

So many times he woke up with problems in bed, nearly caught if someone came to wake him if he overslept or something came up.

He wanted to curse Fuji, but he couldn't, he loved him too much.

Arceus-dammit, he felt like some school girl!

How could this man have this effect on him?

He didn't even expect to find himself attracted, yet here he is, having fantasies in his sleep. He would even space out while awake, thankfully when he's out on a walk, thinking about the man.

It didn't help how awkward it'd get they meet up to turn in reports, struggling to keep up appearances.

He can't risk blushing or becoming a mess if the affectionate man hugged him or simply talked to him.

It was that, and the fact Fuji somehow talked Giovanni into letting them share a room so they could get more work done.

Of course, that had been done long before he realized his feelings for the other.

It had been done not only to do more work regarding the clones, but for the younger man to sleep peacefully. When he tried sleeping alone, he woke up in a cold sweat, sometimes screaming, unable to go back to sleep.

He still couldn't remember who attacked him, who beat him those two days, deducing he must've been drugged. Either something had been slipped into his drink at the bar, or when snatched off the street.

Not that it helps much now, whatever was used is long out of his system, the effect it left in blurring his memories a painful reminder.

But because he couldn't sleep and it began to affect his work, namely starting to doze off at the table, Fuji decided they'd share a room.

The man wasn't afraid to go near him if he heard him calling out in his sleep, begging, sometimes even crying to his faceless attacker to get off.

He wasn't afraid or ashamed to share the bed, keeping his arms wrapped protectively around him, letting him cling like a child all night long.

But now he had a new reason to get little rest…

Fuji simply wanted to protect him from the night terrors, reassure the other that he has nothing to fear now.

Sebastian on the other hand, watching his crush sleep, wanted to kiss him, run his hand through the hair or trace the features of his face.

There was no way Fuji loved him the way he does.

He loves him as if he were a younger brother.

He loves women, without saying a word; he _knew_ that he still thought about his wife, wondering if he could get back with her after Amber's revival.

Fuji's completely pure, like an angel, while he was the complete opposite, tainted, fallen from the heavens.

He doesn't deserve a wreck like him…

Sebastian nearly jumped when feeling a hand pat his arm, staring at the familiar hand, following it up to that same face.

He's walked his crush to the train station that'd take him to the ship leading to New Island to continue working on Mewtwo.

If only this damn train would take him to Johto, he wouldn't mind riding with him just to stay closer longer, then go back. He wouldn't mind the longer time, spending extra money out of his own pocket.

He knows that once the older man's train is out of sight, he'll head back to base to hop a cab and take a flight back to Johto.

"I gotta get going, Shi," Fuji spoke, pulling the man close, giving him a long hug the other never wanted to have end. "I'll see you again."

Being this close, it tore the man's heart apart, making him silently cry, somehow forcing real tears not to fall.

He wanted to tell him right here and now.

He wanted to show him, kiss him so badly.

He wanted to cry, to beg him not to leave.

He wanted to tell him how precious he's become.

He wanted to…

"He…he's dead?" Sebastian gasped, eyes filled with absolute horror.

It was roughly six months since they returned to their labs, only to be brought back instantly, no word why.

The second that he arrives in headquarters, spotting Tyson standing outside the building, leaning against it, he knew something was wrong.

He was smoking, something he did when upset or particularly stressed out and by how long he took the drags, he was upset.

The mere sight made his stomach do flips, wishing he never walked in, walked past the brunette and go straight to the boss' office.

From there, he was led to where they now stood, learning what had happened to the team on New Island.

It was so surreal, he almost didn't _want_ to believe it, that it was just a bad dream, he'd wake up on the plane. He prayed he'd wake up to the Pokégear ringing, answering and hearing the voice of the man he's fallen in love with.

As his eyes slowly trailed down to where his boss stared, staring at the monstrosity the love of his life died making.

Mewtwo…

The Pokémon was apparently asleep, supported by various machines to give energy to the armor he wore.

He had been filled in that this armor was used not only to protect the Pokémon, but help control its psychic powers.

The scientist couldn't help but note that the designs seem to be of Dr. Zager's, meaning what Giovanni said was true.

The sight alone made his heart crack and crumble into thousands, no _millions_ of pieces, his stomach knotting up painfully.

He lost his only friend, the only person who cared for him, protected him from nightmares, the only man he loved.

Why couldn't it have been him to die?

Why leave him in this world to suffer?

Why take away such a wonderful man?

"At least Dr. Fuji didn't die in vain. Mewtwo is perfect. I can only hope that Beta and Omega will be as well once they are done," the leader's voice echoed darkly in the back of his mind.

Sebastian felt himself nod numbly, unable to take it anymore, walking away the second he was allowed to do so.

As he left, he swore he saw the cloned legendary twitch, unsure if it was reflex or it had sensed his internal pain.

He hoped it did, knowing _it's_ the cause for taking away the only man to make him feel truly happy.

He even cursed Arceus to hell, wishing he could literally throw the damn Pokémon into the fiery pits; make it suffer as he's sure Fuji must've.

Before he knew it, he was back in his hotel room, the very same one he and Fuji began sharing, reality finally sinking in.

All the tears he held, the sobs and screams he choked down, they exploded from his very being.

He crumbled to the floor, sobbing loudly, not caring how loud he was, how destructive he became.

Chairs were upturned, curtains torn apart, desk shoved and toppled, scattering any books or papers on it everywhere. The bed was a mess with the sheets and blankets torn apart, the bathroom mirror having been broken.

He didn't care anymore, he didn't care how pissed off Giovanni would be when he gets the bill. He doubted any beating he got could replace the pain in his broken heart, wishing the pain would end, that he could fall asleep and stay asleep forever.

Exhausted from his emotional meltdown, he collapsed onto the mangle bed, sobbing hysterically into the only surviving pillow.

Curling up, he cried harder, his memories of his rape coming back, Fuji unable to chase them away.

It's as if his rapist was in this room now, taunting him that his protector wasn't here, running those horrible hands all over him again.

Fuji wasn't here to hold him, to rub his back and hug him, telling him to wake up, that he's safe, that things will be okay.

But things will never be okay, never again…

He continued sobbing before he had eventually passed out, his adrenaline finally crashing, letting him fitfully sleep.

He felt so pathetic, so weak…

He lost track of how long he stayed in that room, refusing to get up for anything.

He felt his stomach growling for food, but he didn't care, he didn't have the energy to get up. He couldn't even _think_ about eating, convinced it wasn't worth getting up to look for something, to even find something to drink.

At some point, knocks were on the door, but he ignored them, knowing in the back of his mind they'll break in. They had to be agents sent in to retrieve him, to send him back to Johto and finish the cloning project among others.

To hell with it all, he couldn't go back. He'd rather die than continue…

A snap of wood, hinges broken, it was as he predicted, they stormed inside, ignoring how much of a mess he is.

He was too weak to move, feeling them grab him, obviously alarmed by how far he had been wasting away.

At some point, he was brought somewhere, not a hospital, too obvious of a choice with his miserable luck.

IVs and air tubes were inserted; body stripped and scrubbed clean, a feeding tube forced down his throat.

At that, his mind went blank, falling almost in a sleep, going in and out, his strength slowly returning.

Why did it _have_ to return?

He was so close to falling blissfully into an eternal slumber.

He just wanted to sleep forever, forget everything that hurt him in his life.

When his strength returned, it had to have been at least a month, forced into new clothes and taken some place he didn't recognize.

He was so numb, he didn't want to go with the agents escorting him, but knew he wouldn't win.

They were trained for fieldwork, from robbing people and places to scouting, to _actual_ fist fighting. He doesn't have that kind of training to help him escape, to runaway someplace, _anyplace_ than wherever they were taking him.

Arriving to a van, they were driven to an unfamiliar route, kept in the back to avoid him pulling anything funny.

He had an agent on either side, reminding him of his hatred of planes, but he just didn't have the strength to bark at them to back off.

When the van finally stopped, he was dragged out; taking note they were in Saffron City, escorted to a train station.

When did _that_ appear?

Who cares? He sure didn't…

Shoved up the platform, taken to a private cart, hardly taking note of how they arrived, his _escorts_ dressed as bodyguards.

When he was brought inside, made to sit down, they left, either returning to their duties, or were going to wait somewhere else.

A loud noise echoed around him, the scenery beginning to whip past him, realizing they were moving.

After a few minutes, a door opened, footsteps walking inside, a familiar face and his pet taking a seat in front of the broken man.

"So glad that you _decided_ to join me, Professor," Giovanni growled, obviously angry at him. "You gave us _quite_ a scare with that stunt of yours. You realize how much time and money was lost because of your stupidity?"

"Why do _you_ care?" he asked numbly.

"Because _you_ still have work to do."

"You don't need me."

"Oh, but I do, my dear _professor_. You don't realize just how valuable you are to this organization. You know of Dr. Fuji's work, _you're_ the only one who can ensure the completion of Beta and Omega."

"You don't need them, _you_ have Mewtwo. What use do they have? What use do you have for me?" Sebastian partially growled, his depression clouding his judgment of the repercussions he could earn.

"We need _your_ clones more than ever… Mewtwo has escaped," Giovanni answered flatly, taking note of the other's surprise.

"Mewtwo…escaped?" he repeated softly, glassy eyes widening before turning into a dark scowl. "Lucky bastard."

This he muttered under his breath, the other luckily not hearing the comment.

"Yes, he's escaped. Because of that, we now have an extremely powerful Pokémon roaming Arceus knows where. Not _only_ must we recapture him, but if there is a chance he decides to attack, we'll need your clones ready."

"They can't be released early," Sebastian growled, daring to fight his boss much like his beloved Fuji would. "If you do, they'll surely die."

"I know that, so until then, I'm having all of Dr. Fuji's research we could salvage brought to your lab. You knew the man best; you'll be capable of figuring out where he went wrong and prevent it with the other two. I do _not_ want a repeat."

"What makes you think I want to work for you still?"

"Come now, Professor Sebastian, are you honestly willing to throw everything away because someone died?"

"He was my friend."

"Friend or not, you _will_ continue to work for Team Rocket."

"Fuck you."

Angered, the crime lord rose, stalking over, grabbing the other by the front of his jacket, forcing him to look him in the eye.

"You _don't_ have a choice," he snarled, the other staring at him with minimal interest. Ready to strike him, an idea popped into his head, making him grin darkly. "If that's how you feel, if you won't work willingly, then I guess you don't care what happens to your daughters."

Eyes snapped to attention, the shorter male's lips curling to a snarl.

"Don't you dare touch them!"

"Then continue on the project and any others I assign and I assure you that no harm comes to them."

"How do I know you won't hurt them?"

"I can give you a monthly report on their progress. _If_ you agree that is."

Gritting his teeth tightly, he hung his head, knowing he was caught; he was backed into a corner.

"I'll continue…"

"Very good, Professor."

* * *

 _ **Things became bit of a whirlwind, not so much to speed things up, but more to delve into the various emotions he would go through, good and bad alike.**_

 _ **For the love part...I sort of winged it, I never** "fell" **in love, not even having a crush on any one, real or fictional alike. So if I got it wrong or anything on how to portray it, I'll take any critique that may help.**_

 _ **And for his emotional breakdown? Part of it was of my experience, never to that extreme of being destructive and such, but sure felt it from when I lost my grandmother when I was little, a friend a few years back,** and **losing two cats I was particularly close with. So I decided to use the emotions I felt from those times and tried to portray them on someone like Professor Sebastian.**_

 _ **Please read and review**_


	6. Chapter 6

When he arrived in Goldenrod City, the boss returning to Kanto via train, the same escorts from before took him.

He first thought he'd be taken back to his lab where the clones are, but was filled in that he'd be working on some new project.

The idea of work made him sick, but the idea of his daughters' lives put in danger made him feel worse.

If he never grew close to Fuji, this would never have happened!

Arriving at his temporary base, he was allowed to contact his team, informing Davin when he answered he was going to take longer.

The man was frantic, having been worried, but the other brushed him off, the icy mask he once wore reforming itself.

He wasn't going to let anyone else in; he wasn't going to get hurt anymore.

All he has to focus was the safety of his daughters.

Screw the clones, screw Fuji, screw everything around him! But most of all, screw that asshole, Giovanni!

As he worked on the finalization of the project, he worked on the papers and recordings made from Mewtwo's creation, looking for what went wrong.

So far, he found nothing to tie in how Mewtwo grew so out of control, what could've led to his destructive behavior.

That is until he remembered when Amber and the Kanto starter clones died, how Mewtwo had his memories suppressed.

The stress and shock, the fact he had a psychic link with them, it was enough to show him that the Pokémon's mind had _indeed_ been warped.

Having his memories and emotions suppressed, it must've altered his personality, likely confusing him of where those memories went. _If_ he even knew they were missing to begin with.

Sitting in his office, completely alone, hearing Fuji's voice talking excitedly about Mewtwo's progress. He sounded like a proud father, likely felt like one until Mewtwo's awakening and retaliation.

When he finished, realizing that there was really _nothing_ he could do for the clones to prevent a repeat.

He would have to think about it, he knows he couldn't simply _give_ up as much as he wanted to do so. Giovanni wouldn't allow it, no matter what. He has his daughters as leverage, to ensure he _never_ disobeys.

Isolated, his heart growing colder and colder, rarely showing compassion towards others, he finished the Miracle Crystal. He was honestly proud of how it came out through the test trials and research on it. It was the closest with him showing emotions before shutting himself up again.

He presented it to Hun and his new partner, Attila, showing them its capability and what they'll use it for.

It seemed things would go well, that they'd capture a legendary Pokémon, one with nearly unlimited power.

What no one had expected were a group of kids and a man getting in the way, resisting and protecting Raikou.

In the end, they wallowed in failure, the crystal destroyed, Raikou escaping, and most of all, Giovanni livid with them.

The leader had some of his men to discipline them, finding themselves separated and beaten badly. He and Hun got the worst end of it due to their statuses and once pristine records, leaving them limping and blanketed in bandages for days.

The failure was enough to make the man grow colder, yet he couldn't help but feel sympathy for the two agents, the feminine one more.

It didn't help that he only got to _know_ him, become friends with the man because of Fuji, albeit the other _had_ mistaken Hun for a pretty girl.

He knew about Hun, but said nothing, mostly out of surprise when the other reacted quite violently, taking after his friend.

It was rather awkward and strangely funny, watching as they ran about, the feminine man threatening to show the much older man what a _real_ girl looks like.

Somehow, Hun managed to chase Fuji up a rather tall lamppost, the two looking completely ridiculous.

It was only thanks to Tyson calming the smaller man and managing to help the scientist down, things began to improve. Fuji apologized and somehow got Hun to join their little circle of friends.

It was only then they learned that the only reason he was so active, not level headed was because he had just left a bar. His last partner had dragged him out for drinks to celebrate a success and was pretty wasted.

They didn't want to risk him getting hurt, so offered for him to stick around, getting to know one another better.

It had to have been the best decision for Hun, as he now had people he could freely talk to when not on the job.

Although it wasn't right away, it was only seeing how they interacted, finding how comfortable they were around one another, he began to open up.

But because he was called out often, they didn't get to see him much, but when they did, if he wasn't busy, they'd hang out.

They would fill each other in on how they're doing, making jokes, having drinks, acting like normal people, not part of some criminal organization.

Hun was far different than they would've expected from such a high ranked member, higher than all of them.

It was then they learned he acts this way _because_ of his looks, having often been harassed when he had been a lowly grunt.

But to keep people from taking advantage of him, he studied as much as he could, so he would rarely have to rely on others. He kept a cool head most of the time, things rarely bothering him. If they did, it was either under immense stress or as their first meeting, getting him wasted.

He gave no hints of being girly, even owning a brutal Pokémon, something he always owned since before joining Team Rocket.

He told them that he found Steelix when he lived in Sinnoh on an island, finding the brutish creature amazing and wanted it. And with much planning and placing traps, he was able to subdue and capture the Pokémon, making it his.

Oddly enough, he was rather fun to have around, knowing good jokes, having plenty of stories to share.

Although, the closest they would get to Hun acting _remotely_ feminine is if he ends up having too much to drink and passes up. And a sleeping Hun is a rather adorable sight to behold, but none would admit without enduring his wrath.

Reminiscing in these memories, Sebastian could feel bitter tears forming in his eyes, trying to blink them away. He loved them for the fun they shared, but hated them at the same time for the pain they caused.

He wanted to forget it all, forget all Fuji did for him, the joy he gave him, the friendships he made with his help. He had to forget it, push them away as if they were nothing, unsure how they even _feel_ about their friend's untimely death.

Hun hasn't said a word and he hasn't seen Tyson since that day…

A knock resounded on the door, causing him to look up, not bothering to respond as he watched it open anyway.

In walked the very agent he was thinking about…

"Professor," he greeted curtly, the other giving him almost a lazy look.

"What is it?" Sebastian asked rather coldly.

Both flinched at the sounds of glass breaking and explosions, the older of the two cursing as he spaced out, forgetting to shut the recording off.

With a swift hand, he turned it off before any more could be heard.

"I apologize, I didn't know you were working," the younger man apologized, his own icy mask slipping away.

How many of them wore masks in this Arceus-forsaken organization, hiding from the world, hiding from themselves even?

"It's alright," he numbly answered, turning to put things away.

He got all he needed from them; he made separate notes to take back once he finished another project dropped in his lap.

It was sudden and surprising after his last failure, but decided not to argue, not with his daughters in possible danger.

So long as Giovanni has them, there was nothing he _could_ do…

"I came to inform you that something came up regarding Mewtwo."

"What is it?" he asked, unsure if he honestly _wanted_ to know.

He heard that the clone had been found, but because he was needed to finish the Miracle Crystal, he was barred from participating.

"I'm not exactly sure. I was in another region when I was called back for the mission, but my plane was delayed."

"What happened?"

Shifting almost unsurely, he spoke, "No one appears to remember him."

"This better be a joke."

"It isn't, I even looked into it and there's _nothing_ about Mewtwo. All the data, all knowledge about him, all of it is gone. There's nothing about him or Dr. Fuji, or _anyone_ from his research team."

"How did this happen? Giovanni wouldn't just give up!"

This had to be a sick joke! It was too good to be true, to believe he could possibly be free, that he might be able to find a way out of this.

"I know, but I honestly have no clue what happened. By the time I arrived, it was over, they were returning to base. They had no recollection of what they were doing."

"Why are you telling me?"

"Because I know how much you cared about Dr. Fuji, how badly his death affected you."

Damn him and his perception, he wasn't sure if he knew about his crush, but didn't care, not like anything could be done about it.

"But how could they have forgotten?"

"I have a feeling that Mewtwo erased their memories, to hide his existence to avoid further pursuits. Even the files back in headquarters in Kanto are gone, so he must've gone there and subtly destroyed them."

"Somehow I'm not surprised."

"But Giovanni _still_ knows about your clones though."

"Dammit."

It _was_ too good to be true, how Beta and Omega avoided Mewtwo's detection was a sick miracle. And if knowledge about them is still around, that means his team still remembers, working on them, _worrying_ about _him_.

"Professor Sebastian, what do you want to do? The data you have…that's all that remains, the only proof of Mewtwo."

"I got all I need from it. Destroy it, all of it and never speak of it to anyone. If there is _any_ information regarding Mewtwo, report only to me or don't say anything at all. Do you hear me?"

"Professor…"

"Don't make me repeat it!"

A crack in his mask showed, the other seeing how much the order pained him, erasing the last thing relating to his late friend, his love.

"Of course," Hun answered, walking over, collecting everything slowly.

When he got it all packed, a single box filled with tapes and a few notebooks that had survived the destruction.

Before he left, he decided to ignore normal protocol, hugging the other, feeling him stiffen at the contact.

"I miss him too," he whispered before pulling away, walking out with the box.

"Damn you, Hun," Sebastian growled, tears he believed were long gone forming once more. "Damn you…"

It was a struggle performing his jobs, but managed to complete the next one, the Evolution Inducement Ray.

He had to pretend to enjoy the fruits of the labor, hiding behind his mask once more, doing everything in his power to ignore the cries of the Pokémon.

For this project, Project Revolution, it was on its way to possibly succeeding, even reuniting with Tyson.

But he treated him as he would others at the lab; the man had no real memory of how they became friends. He was present when Mewtwo wiped their memories, so why risk bringing it back up?

Yet once more, it had been foiled, another group of kids, incompetent grunts, and worst of all, Lance, the champion of the Kanto and Johto regions.

When word came back to Giovanni, he was furious, much like how he had been when the Miracle Crystal failed.

But instead of another beating, possibly killed for his failure, he was merely threatened not to screw up again. If he did, his daughters would pay for _his_ incompetence.

The thought greatly chilled him, unable to keep up his stoic appearance when hearing the threat.

Eventually he was allowed to return to his main lab where the clones had been growing and may still be growing.

He didn't expect his team to greet him with such joy, wanting to push them off, seeing how relieved they were to have him back.

It was becoming too much, he wanted to strike them, his hand clenching into a fist, ready to raise it and hit the nearest body.

All thought stopped, his eyes landing on the test tubes, seeing the clones sleeping in their respective tanks.

They were bigger, _much_ bigger than last time, now the size of small children, possibly a toddler.

Falling to his knees, realizing what he almost did, he stared at the clones, unable to hold back his emotions.

"Professor!" Joel's voice called out, grabbing his shoulders. "Are you okay? Do you need to lie down for a bit?"

Turning to him, he gave him a bitter smile, "I think I'll be fine. I was just surprised by how much they've grown."

"They _have_ grown a lot…" he chuckled softly as he helped him to his feet.

"I'm so sorry, for being gone so long."

"It isn't your fault, Professor. You were busy on other projects."

"And they were failures…" he laughed, his voice hollow.

" _They_ won't be… We got the copies of the data you collected with what happened with Mewtwo. So long as they don't endure anything he had that day, they'll be fine."

"No they won't…"

"What do you mean?" Cassie asked as he ushered them to a room, everyone sitting down at the table.

"Do you know _why_ Mewtwo escaped?"

"N-no."

"Giovanni was trying to make him into a weapon. To use him to take over Kanto one day, possibly the entire world."

"Oh Arceus…"

"So…so we've been. All our work into them was for…"

"I'm afraid so, I'm sorry for never telling you."

"This is insane!" one of the more unfamiliar scientists cried out.

"It is, it really is," Sebastian answered, the numbness threatening to return. "I'd have the whole thing unplugged, sparing them…"

"He won't let you?"

" _He_ has my daughters, he threatens to have them harmed, killed even if I failed again. They're the only family I have left!"

The tears he tried to fight back came, his face wet as he buried his face into his hands, shoulders shaking.

"Professor…" Davin sighed, understanding his pain. "We'll continue with the project then, but there must be something we can do for them."

"I don't know. I haven't been able to think of anything."

"Maybe we could alter their personalities?" another scientist offered, others looking up including their boss.

"What are you talking about?"

"Well, not to sound sexist, Cass, but they _are_ girls. At least at a young age, they'll be more passive on an instinctive scale. If we create a formula to increase it, then they would have little reason to lose control over their anger."

"But in turn would cause them become weaker and in Giovanni's eyes, useless. He would have them killed, we included," Sebastian added bitterly, "unless…"

"Do you have an idea?"

"I think I do."

Getting up, he went over, comparing the notes he wrote down regarding the serum used on the male clone.

"Mewtwo wasn't _born_ cruel nor was he really _made_ cruel," Sebastian started with his team listening intently. "When the other clones died, he had some sort of link with them that sent him nearly over the edge, one that would've killed him from the emotional shock losing them so quickly, so suddenly. The intention to suppress it all was good, but forgot about the real importance of emotions."

"Mewtwo was still in the chamber in all that mess. He never woke up until he was fully matured and broke free," one of the others gasped, recalling the notes and rumors sent their way.

"Exactly, he was fully matured with the emotions of a child. And what do children do when they're confused, upset even?"

"They end up throwing tantrums!"

"And Mewtwo threw one just like any child, a very destructive one…" he spoke, his voice softening as he recalled those recorded screams. "He carried the intelligence of an adult, could speak like an aristocrat if he wished. He has the power to wipe memories from people and electronics. And while calm, _appears_ mature, and may _have_ been most of the time. But the second you make him angry…"

"He'll lose all composure."

"Yes, at least back before he escaped Giovanni. I can't be certain, but it appears that he _had_ matured to some degree. The fact he didn't outright kill Giovanni and his men when they came to get him shows that."

"So what are you going to do?"

"For now, nothing, if we make them passive, as I said, it'd only put them in danger as much as ourselves. What we need to do is make sure that when they're ready, we can keep them calm. By doing so, we can teach them how to use their emotions properly, hopefully teaching them enough so we don't have a repeat."

"And we'll have to watch what we say around them," Joel sighed, crossing his arms in deep thought. "They could misinterpret what we say or mean, leading to one hell of a temper tantrum."

"Yes, that is true…" the man sighed, feeling a hand land on his shoulder.

He almost believed it was Fuji, turning around with hope in his eyes, only to lower his head, seeing it was Joel.

"We won't let it happen," he reassured, the other somehow comforted by it.

Soon after, he was filled in all that happened, between various activities, including Cassie and Davin becoming engaged.

He realized just how much he missed their company, how badly he missed his friends, congratulating them.

Within a few more months, the clones were taking on a more defined appearance, showing while looking like Mewtwo, were different.

Both were more slender than the first clone, faces narrower, revealing their sex far better than having to physically examine them.

They were still asleep in the liquid, looking so innocent and peaceful, completely unaware of the horrors around them.

Sebastian had long since given up trying to hide his feelings, trying to hide behind some icy mask. His team saw through it, they knew he was still hurting losing Fuji; they _all_ were in their own way.

He gave up trying to blame Fuji for leaving him like this; it wasn't as if he meant to hurt him in the end. The clones were innocent; they had no blood on their hands, only Mewtwo did. _He_ took his love, not them, why blame them?

He found himself getting closer to his team, sharing secrets, namely why no one outside themselves don't remember the original Mewtwo or his creator. He shared with them more of his personal life, learning more of theirs.

Who would've thought that he'd find the strength to open himself up again to other people?

One more thing to be forever thankful for, knowing Fuji was the cause to find that lost strength, to learn to trust again.

* * *

 _ **Some more emotional stuff, but also some growing up if you think about it.**_

 _ **While I know that in the Japanese version, Hun and Professor Sebastian didn't know one another, least from what I read, I only got to see the Dub version, so yeah, going with that. Plus it was fun at least writing how they in a sense** do **meet, adding their own little quirks that may or may not exist.**_

 _ **As for the Mewtwo thing, it was just my own observation, though I could be wrong to an extent. I never** really **got to see the special prequel or however it's called regarding Amber and Mewtwo's encounter.**_

 _ **I heard, read, and saw bits and pieces in Japanese with subtitles. So figured, being what he endured and what was done, it would make him emotionally unstable, not knowing really how to control those same emotions.**_

 _ **Please read and review**_


	7. Chapter 7

As his focus returned to the clones and Mega Evolution, Sebastian found the latter absolutely fascinating.

The use of two stones, a Key Stone, and a Mega Stone that has made it possible for certain Pokémon to unleash immense power.

Yet the power is not only temporary, but cannot be unleashed less the bond between trainer and Pokémon is perfect.

Many appeared during a conflict between two of Kalos' legendary Pokémon, Xerneas and Yveltal, many evolutionary stones changing into Mega Stones. They also have appeared during certain meteor showers, evidence from old tablets and carbon dating some of the stones found.

"I wish I could see what one of these Key Stones and a Mega Stone is capable of," Sebastian grumbled as he finished reading another book.

This one spoke about all the individual stones, what affects they have on the Pokémon holding their respective stone. It talked about certain moves or abilities that they may acquire because of it, and much more.

"They aren't easy to acquire I'm afraid," Joel spoke, seeing the other looking somewhat frustrated. "Even _if_ you found one, the other would be just as difficult, and that's if you even _have_ the correct Pokémon."

"So I've read, the Mega Stones seem somewhat easier to find though."

"For the most part, yeah, they are. They could be found just about anywhere, some even found as blanks, having no synch until a Pokémon makes contact."

"How so?"

"Take Charizard, if it's in conflict and makes contact with a _blank_ stone, it has a fifty percent chance changing into a Charizardite X or Charizardite Y. Exactly _how_ or _why_ that happens, no one is certain, including why there could be blank Mega Stones to begin with."

"Rather strange that it has two possible forms though."

"Not really, Charizard are incredibly powerful, so it splits that power based on the trainer and Pokémon's preference. At least that's what some researchers theorized before I came here. I'm sure that there are others similar to a Charizard's power, but haven't been discovered yet."

"Heh…if there was a way to _get_ one, I have an idea what ones I'd like to get, at least to see what they actually do."

"Really?"

"The Steelixite, I know a friend who owns a Steelix, and they have a rather strong bond the last I saw them. If one could be gotten, I'm sure he wouldn't mind having it, not only getting a boost in power, but help out with our studies as well."

"Well, just because they have a strong bond doesn't mean they can handle Mega Evolution. It's a huge amount of power they get; it could potentially drive one or both of them insane if they're not careful."

"I see, that would be problematic."

"But being that we have to work on this anyway, I'm sure you could convince Giovanni somehow to let him go. That is, if your friend is part of Team Rocket."

"He is, and he's trustworthy," Sebastian answered before reassuring the other when seeing his concern.

Like that, he made calls, taking a train to return to Kanto to speak with the boss personally, calling Hun as well to meet up with him.

Arriving at the rebuilt headquarters, he was surprised to see Attila as well by the feminine man's side.

"You two are still partners?"

"Of course, despite what happened with the Miracle Crystal, we still made a nice team. Unlike _most_ partners, we actually get along," Hun chuckled as they walked in. "So what is it you wanted me for though?"

"It is part of a research I'm doing called Mega Evolution."

"Never heard of it," Attila commented, the others ignoring him, mainly since he spoke for his shorter partner as well.

"It's a bit of an unusual phenomenon. It's mostly known in a region known as Kalos, but began popping up in various locations in Hoenn."

"So what does it do?"

"There are various stones, one set known as Key Stones trainers carry, the other known as Mega Stones that a Pokémon carries. One of these Mega Stones is known as a Steelixite, and if I recall, _you_ have a Steelix."

"I see, so you want to see one in action and chose me?"

"Exactly, if you and your Steelix are able to control it, you would be much stronger than you are currently."

"I like the sound of that and I'm sure Steelix would too," Hun laughed softly as he held the Pokéball containing his Pokémon.

"So none I could use for mine?"

"There haven't been any found to Mega Evolve a Skarmory or Muk as of now, but those may simply have yet to be discovered."

"Well if you find out, let me know, wouldn't mind getting my hands on one or two if I'm lucky."

"Even if you do get both Mega Stones for them, if they exist that is, there are some minor problems relating to Mega Evolution."

"How so?"

"For starters, you could only maintain it for a brief while and only with one Pokémon at a time. From what I've learned, when you activate this unique evolution, it drains not only the Pokémon, but trainer as well. Therefore attempting to draw more for multiple Pokémon…"

"Could pose hazardous for the trainer as well," Attila grumbled, grateful to have been filled in on that at least.

"Exactly, and I don't want to put you two or anyone in unnecessary danger until we have more facts about it."

"Not like you to give a damn," the blonde teased before getting elbowed by his partner, silencing him.

Walking inside, they reached Giovanni's office, the scientist knocking just loud enough to be heard.

"Come in," his voice called, the tone indifferent.

"Sir," the two agents greeted, the other saying nothing as he walked in, taking a seat, his mask reformed for the sake of this meeting.

"What do you want, Professor?"

"I've learned as much as I could in regards to Mega Evolution, however, there is still much I don't know about it. I'd like to send a couple of agents, ones with strong bonds with specific Pokémon to try to obtain these stones."

"Is that why you requested for Attila and Hun to come here?"

"Yes, Hun has a strong bond with his Steelix and by chance, there _is_ a Mega Stone specific for that Pokémon. If their bond is as strong as it appears and are successful getting a Key Stone _and_ a Steelixite, I could get much more information watching them in action."

"I see, but what does it do for me?"

"Mega Evolution, while temporary, if a Pokémon and its trainer have a certain bond, they are able to unleash tremendous amount of power."

"I think I'm beginning to understand," the man smiled darkly, the gears already turning on the possibilities with Mega Evolution. "Is there any specific place to go to find these stones?"

"The Steelixite I cannot be for certain, but there have been rumors of some found in isolated pockets in Hoenn. As for the Key Stones, they are mostly obtained from Gurus or certain _trainers_ you could say. I haven't found any book that says where one could find one by chance. Either the authors don't know or have taken some sort of vow of silence relating to their possible locations."

"Gurus?"

"These stones aren't given out to simply _anyone_ with a Pokémon, one capable of Mega Evolution. The trainer must prove themselves to that Guru, so it may be difficult to know if Hun will be successful. Trying to take it by force may prove useless. They are said to be _exceptionally_ powerful trainers."

"I see, so you would need Hun to likely go alone with a completely new identity then?" Giovanni asked curiously.

"Close, I'm positive the Guru would have a psychic type, regardless if it's capable of Mega Evolution or not. They could use it to sense if Hun is a threat or harbors other motives. He would have to be honest in such a way that any lies that _are_ told are believed even by himself."

"That makes sense," Giovanni grumbled, petting his Persian before a thought came to mind. "What of these certain trainers you mentioned?"

"I wouldn't recommend looking for these trainers. Many of them are powerful, most being former or current champions such as Steven Stone or most notably, Caitlin Panthera," Sebastian warned, seeing an angry twitch at the woman's name. "Though some are likely gullible, so one _could_ have more hope in getting a Key Stone if encountered. So long as they don't have knowledge about Hun's involvement in Team Rocket, he may be able to get it easier."

"Look into it; I'll have you three sent off for Hoenn to look for this Steelixite. If you find others, get them. Even if they're basically useless, they _could_ have potential on the black market for collectors."

"Of course," Sebastian answered as they began to leave before stopping. "What of the Beta and Omega project?"

"They can continue without you for the time being."

"Time _is_ winding down, they cannot stay in those tanks forever and I _insist_ I'm there for when they're ready to come out."

"Of course, if word comes that they're due, you'll be first to know."

"And I'll still get the reports?"

"Of course, Professor."

Once they were out of the office and sent to get ready, the professor made a stop to call his team about his sudden absence.

They were a bit upset, but knew that if they're to make progress on the Mega Evolution, he would likely have to go into the field itself.

With that, they found themselves on a private jet so they could freely discuss the best course of action, glancing at the maps given.

Surprisingly enough, they weren't there for long, they not only found the proper Mega Stone, but two blank stones. They were obvious; having the same markings as a normal Mega Stone, but were milky and translucent. Other Mega Stones were found, not a whole lot, finding a total of fifteen, ten of them being duplicates.

Now all they needed was a Key Stone, Hun in the duration working with his Steelix, to ensure their bond truly was strong.

It was obvious he was nervous, having been told of the possibility of him or his Pokémon, even both going insane. He was determined to avoid it, reassured that if such a thing went wrong, they would knock him out as well as Steelix.

Attila showed surprising craftsmanship, creating a perfect harness for Steelix to wear, carrying its Mega Stone without risking harm to it.

What none of them expected was to discover a green serpent flying by, recognizing it as the legendary Pokémon, Rayquaza.

Giovanni learned of their discovery, ordering them to capture it, having done research himself and found it has some connection to Mega Evolution as well.

With that, they took after the Pokémon, other scientists present already at work, the grunts using a combination of missiles and Pokémon to take the dragon down.

Lives were lost by its retaliation, a majority being Pokémon sent out, but in the end, the powerful dragon was detained.

"I don't believe it," Sebastian whispered, in awe as he walked up to glass wall separating him from the Pokémon.

He heard footsteps behind him, internally flinching when the Pokémon let out a pain filled roar when shocked by the restraints.

"We finally caught a legendary Pokémon…" Attila spoke, unsure what to make of the whole thing. "But what do we do now?"

"We would need to study it, but I need it unconscious. Having it attempt attacks or twitching from the shocks won't do us any good," Sebastian spoke as he began working on the computer.

Before long, gas filled the room, the Pokémon hacking a bit before starting to get tired, but the shocks prevented it from fully falling asleep.

Hitting a few more keys, the shocks stopped, the Pokémon falling completely unconscious, slumping into a hopefully peaceful slumber.

Picking up a phone, he dialed a number, holding it to his ear, "Yes, I need a medical team brought in to examine Rayquaza for internal injuries. We need it healthy for studies and any possible uses it could have."

Listening for a bit, he hung up, turning to the other two with a frown, leaning against the railing.

"Are they sending people up?" Hun asked.

"Yes," he sighed as he glanced up at the Pokémon, a look of pity on his face.

"You really seem different, Professor," the blonde spoke, placing a comforting hand on the other's shoulder.

"I'm fine," he answered, pulling himself free as he went to a room to change into proper scrubs.

When he came out, others arriving, fully changed as well, he led them inside, telling them what to look for while taking samples.

"Be careful!" he snapped angrily. The dragon's face twitched in pain, spotting one of the scientist take a rather large tissue sample. "I have the electrical currents shut off, if it wakes up, we're dead."

"Why the hell did you shut them off?" Namba's voice shouted, near the tail end of the dragon.

Ignoring him, he had the hover pad carry him up to the face of the beast, refusing to let the other novices near it.

Reaching a hand out, he gently petted the dragon's snout, warm breath blowing past him as it continued to sleep.

"I'm sorry," he whispered as he used a device to help pry its mouth open.

With tools set up, he began to take various samples of plaque, lightly scraping the gums and tongue for tissue.

"What's this?" he muttered, finding something embedded between some of the fangs, managing to dislodge it. "A rock? No, a meteor!"

But there was something strange about it, it was a small piece, signs it may have been chewed on before swallowing.

Why would Rayquaza eat meteorites?

Could its digestive system be similar to certain fowls and bird like Pokémon?

Getting what he needed, he had the mouth close, now working on getting a mucus sample from the nose, paling when seeing an eye cracking open.

"Shit!" he cursed, feeling his body shaking as it began to wake up.

A soft growl escaped before falling back to sleep, clearly too tired to fight, letting him breathe a sigh of relief.

Forcing his body to calm down, he got the rest of the samples he needed from the nasal cavity and a few from around the eyes.

Finally done, he ordered everyone out, letting the Pokémon rest, deciding not to let it endure further shocks. It was a risk, but if it began to cause a ruckus, he could hit the gas, knocking it out.

"Tch…pretty ballsy, sticking your hands in its mouth like that," Namba taunted, seeing the man shaking a little still.

"And if I hadn't, I wouldn't have found _this_ ," he retorted, revealing the drying meteorite fragment.

"Why the hell would that damn lizard eat meteors?"

"I'm not sure. Next time it has a bowl movement, collect samples and go through them. There could be more and perform studies on the stones."

Glaring at the orders given, he reluctantly obeyed, though was going to make others do the dirty work than himself.

Going to his private office, Sebastian sat down, deciding to take personal interest in the space rock.

"Very peculiar," he whispered as he continued doing research, calling up his Mega Evolution specialist, wanting to ask him questions. "Is Joel there?"

 **"** **Professor Sebastian?"** the man yawned, the other forgetting that it's a different time zone.

"Sorry for calling so late, but I found something of interest. I'd like you to look into some of those lore books you brought regarding Mega Evolution and its origin."

 **"** **Any specific?"**

"Anything regarding meteors."

 **"** **Meteors?"**

"We managed to capture a Rayquaza and when we were examining it, I found a meteor fragment stuck in its teeth."

 **"** **C-captured Rayquaza?"** the man stuttered, fear evident. **"** **Sir, you have to release it immediately!"**

"What?"

 **"** **Because it may already possess a trainer!"**

"Shit, I can't believe I forgot," he growled, slapping a hand over his face.

He remembered reading about that in the papers sometime back as well as on some news channels.

It happened after an incident at the tropical islands, the Orange Archipelago, information revealed to have been caused by some _collector_ as he called himself.

Because of the hunter's actions, he inadvertently created a disruption with the global climate. And it only grew worse with each bird captured or when they began to fight each other upon being freed.

To preserve certain species of Pokémon, namely those of legendary status, any wild ones found are captured by selected trainers.

Instead of containing them in the Pokéballs though, they are removed from normal rotation, allowing that trainer to in a sense carry more than six.

The Pokéballs were designed by a combined effort of several companies, Silph Co. in particular.

They would mark it as the trainer's to avoid others attempting capture for whatever reason. Because some are needed for environmental purposes, they've been designed so they could technically remain in the wild. Their Pokéballs have no real hold other than preventing others from catching them on sight.

But because there are poachers, some not knowing or not caring, trackers were put in to monitor the Pokémon's health and location. If there are any known for wandering the region or planet even, they would be monitored extra closely. That way, if they suddenly stopped and didn't move for so long, a team would be sent to examine, if not the trainer his/herself if they happen to be in the area.

He shuddered at the idea of this Pokémon's trainer coming here, having a gut feeling _who_ may own it.

There are only a handful of trainers who would be trusted with this sort of task, to risk their lives to protect such powerful creatures.

He can't take the risk, not with his daughters' in danger, not with the clones still developing. He just can't risk it…

"I'll have it released immediately before anyone finds out we even had it."

 **"** **Just be careful, they're known for being vengeful."**

"I wouldn't be surprised…"

Disconnecting, he nearly ran straight to where the dragon was kept, getting things ready for its release.

"What the hell are you doing?" one of the scientists shouted.

He saw that some of the restraints releasing their hold on the dragon's arms, grabbing the other before he could release any more.

"We have a very high chance, and I mean _very_ high chance that this thing has a trainer!" he shouted back, his heart beginning to race. "I rather not take my chances finding out if it's true."

"You don't have that kind of authority!"

"Do you _want_ to run the risk of someone like Panthera storming in here to take her Pokémon back?"

"How are you so sure that this is hers? That it even _has_ a trainer?" Namba asked, walking in with a scowl on his face.

"I spoke with a member of my team…"

"Who gave _you_ permission to make outside calls?"

Hearing the commotion, Attila and Hun were by the professor's side, seeing a standoff forming.

"What the hell is going on, Professor?" the silver haired man asked, staring between the two.

"Professor Sebastian here is planning on releasing our precious cargo," Namba stated, seeing the two look stunned. "How _are_ you so certain of what you say? That your team is so certain?"

Giving a frustrated growl, he told them all that he could remember, specifically the Orange Island incident. Many paled, some recalling it, feeling stupid for forgetting something so important such as that.

"Dr. Namba, sir, I have to agree with the professor. If there is a chance…" Hun started before the other shot him a look.

"Giovanni ordered us to capture it and that's exactly what we've done. Until he gives the authority, we're keeping it," Namba stated, walking past the scientist.

Hitting a few keys, having the restraints return, he began using the electrical shocks to keep the Pokémon still.

"Now, if you're done standing around like a bunch of Quagsire, get back to work!" he snapped, many running off.

"You're making a _big_ mistake," Sebastian growled, storming off.

Hearing the two agents at his heels, he was mildly grateful they stuck to his side than blindly sticking to Giovanni's.

"What are we going to do?" Hun asked, grabbing the other by the shoulder to make him stop. "Professor!"

"We got what we need. If Dr. Namba is going to be a fool keeping Rayquaza; I'd rather not be around when its trainer shows up."

"Then we should get out of here then," Attila smirked, "might be a good lesson for the good _doctor_ to learn some humility."

"I doubt he has the capacity to know what that means," Sebastian joked dryly as they packed their things.

* * *

 _ **That whole thing regarding Mega Evolution and how the blanks stones I came up with. Right there its so new and from what I** could **find out, there's really not much. We don't know if** every **Pokémon is capable of Mega Evolution or its a select few.**_

 _ **And the blank stones, again came up with that since we don't know how some of these evolution stones mutate in a sense, let alone into what we know as Mega Stones. We don't even know where Key Stones come from, if also from various evolution stones, or something else entirely different.**_

 _ **If there's anyone who has a better idea, namely having seen the anime or their own theories would be great.**_

 _ **With the legendary Pokémon, again, just made that up too, though in some ways** does **make sense for the Pokémon League(s) to do that. It** would **likely help protect certain species without flatly saying it, so not all, like Ash would know right away. Plus it's recent, so it wouldn't hit everywhere just yet** **and a number of trustworthy, powerful trainers would have to be chosen.**_

 _ **Hope that this makes some sense.**_

 _ **Please read and review**_


	8. Chapter 8

It was as Sebastian predicted, barely a week passed after he, Attila and Hun left, the ship carrying the captured Rayquaza was attacked.

Rumors that it was a ranger with several Eevee was heard, whether it was true or not didn't matter. The Pokémon escaped in the end, Dr. Namba humiliated of losing such a powerful and rare beast, for not heeding his warning.

Sebastian was back at his research lab, the two going off to Kalos to keep a low profile and see if Hun could get lucky obtaining a Key Stone.

The blank Mega Stones were kept with him, to study their properties and find out why they appear as such than others such as Hun's Steelixite. The remaining Mega Stones, while a few were kept, the rest taken for appraisal.

Sitting at his desk, Sebastian stretched his sore limbs, deciding he needed to take a breather, ready to head outside.

But before he does, he had to return the stones to their storage unit to avoid damage or worse, getting turned into official Mega Stones.

Passing the freezer, he felt himself pausing, the box in his arms, the two stones safely tucked inside.

Something in the back of his mind was telling him to go in there, the voice becoming too strong, unable to resist.

He quickly put the stones away to where they needed to, returning to the freezer and going inside.

Looking through some frost covered cases; he found what he was looking for, tears beginning to form.

Amber's DNA…

He completely forgot about having this, recalling the promise he made to Fuji.

Should he still uphold that promise even if the man's dead?

It was the least he could do…

Taking the samples, finding much had degraded, having sat so long, he pulled just enough to start cloning.

"What are you doing?"

"I'm fulfilling a promise I made, Davin," Sebastian smiled bitterly.

He made the finishing touches before activating the third unused tube, grateful it was kept in pristine condition.

"Promise?"

"Yes, do you know why Thomas worked here?"

He had no reason to hide how much the late doctor meant to him, the others seemed to have figured out enough. Even if they didn't know he was actually _in_ _love_ with the man, the strong bond was still there.

He even convinced his team that they didn't have to use titles, they became familiar enough, become friends even. The only time they would use their titles, at least for the leading professor would be if they had _unannounced_ guests.

"Not much."

"He lost a daughter a long time ago and wanted her back, to give back the life stolen from her. He asked me to bring her back if he couldn't."

"I see… You really cared about him."

Flinching a little, he gave the glass a nervous smile, "I did… I really did. I just wish I told him just _how_ much he meant to me."

"I'm sure in some ways he knew," Davin reassured, patting him on the shoulder, a comforting smile on his face.

"Umm…is there any way that we could help too?" Cassie spoke up, grabbing the pair's attention, having overheard. "A human _is_ different than a Pokémon."

"That and she had been sick in her time alive…"

"Then that would make it harder to clone her."

"I know…"

"Then let us help."

Others stood with her, the looks on their faces showed they were going to help, put all their knowledge and skills to bringing a human back.

"Thank you, all of you," Sebastian smiled, a rare look he shared with so few.

Like that, they began to work on Amber's DNA, using the old notes Fuji had kept about her, looking at the different methods he used in each attempt.

Finding what may work, they got to work, following the same method they're using for the other two clones.

If all pans out, they would be the first to successfully clone a human, bringing her back to life.

With much discussion, they decided that unless necessary, they planned on taking her out when she was an infant.

As for _who_ would raise her, they discussed it as well, deciding that her main parent would be Sebastian.

While he never got to raise his _own_ daughters, he already knows parenting, the rest having no clue, not even having younger siblings.

But most of all, this was Thomas Fuji's _daughter_ , Sebastian knew him best, would know enough how to raise her properly.

When he was first told about it, he wanted to argue, but seeing their determined faces, he couldn't help but see Fuji in their faces.

If he were here now, he'd agree too, he was sure of it, especially if he had known he was going to die so soon.

Maybe he already knew? It would explain why he gave him those samples when they began on their projects.

As the months crawled by, the team monitoring the older clones, kept their eyes on their newest addition. If they mess this up, there was no second chance; it was all or nothing now.

Looking at the fetus, there really wasn't much, seeing such a tiny thing one would almost mistake as a wad of chewing gum.

It made them think back to when Beta and Omega once looked like this.

However, the joy they shared, the excitement they held was soon cut short.

Giovanni walked in unannounced, several grunts and high ranked officers nearby, one of which was Tyson.

"Hello, Giovanni," Sebastian greeted through clenched teeth.

He was doing everything in his power to keep his disgust with the man hidden, eyes narrowing further when seeing his ex-wife standing with him too.

"What's the progress on Beta and Omega?" he asked, walking over to look at the floating clones.

"They're doing well, it will be another few months before they can be taken out," he answered, keeping his tone even.

But all that composure left when Meiya discovered the third active test tube, seeing the barely developed fetus.

"What on earth _is_ that?" she asked, obviously disgusted.

"Care to explain what you're doing here?" Giovanni growled dangerously, making the other start shaking.

"I found extra samples of Mew that weren't used. Rather than risk them being ruined by age, I figured it would be beneficial to clone a third one," he lied, praying the man would buy it.

He could always lie about it dying, and when it came to Amber's rebirth, just claim he or one of the others had a fling with Cassie. If that didn't work, they could always say they found her, having taken a walk for fresh air and heard crying.

He knew all the spots in the area, knowing some were common for hikers, but rough enough to deter them from going further.

But much to his horror, he had forgotten that the powerful man before him isn't some moron to be toyed with.

"Don't lie to me; I know _exactly_ what a human fetus looks like. Tell me, Professor, what exactly _are_ you planning on doing with it?"

Lowering his head, unable to meet the man's gaze, "I made a promise."

"A promise? To whom?"

"An old friend. I promised I'd bring his daughter back."

"So you're wasting _my_ money on a silly promise?"

"It isn't silly; there are other benefits to cloning her!" Sebastian argued, recalling Fuji's words, the hopes he bore. "She died from an illness. Her father found the cause and made a cure, but it was too late. He wanted to bring her back and asked me to help him accomplish it! She'll be the first ever human cloned, one who had been sick before, but now completely cured!"

"Enough of this nonsense, I want it destroyed. You've wasted enough of my money on this useless experiment."

"No… I won't let you kill her," Sebastian growled, stepping in front of Amber's tank, determination in his eyes. "Do what you want with me I don't care. But I won't let you hurt her!"

"How courageous of you, Professor Sebastian, but you forget one thing," Giovanni laughed, obviously amused.

With a snap of his fingers, Meiya and other Rockets came in, restraining the scientists that tried to resist.

"No! Don't do this! I'll destroy Beta and Omega if you do this! I swear it!" he screamed, pinned down, watching with desperate eyes.

"Giovanni, sir, isn't this a bit much?" Tyson tried to argue, the other shooting him a dangerous look that froze him in place.

"Not at all," he answered, hitting a switch, watching as the machine keeping the fetus alive shut down.

"You bastard!" Sebastian screamed, tears coursing down his face.

He struggled to break free, knocked out by a sharp kick from the woman he hates with a burning passion.

When he finally woke up, he found his team lying on the ground, slowly coming to as was he.

Tyson had stayed by his side, a sad look on his face, not knowing just _how_ much pain he was in.

Whether he stayed on his own free will or stayed due to orders, the man wasn't sure nor really cared that much.

He looked at the tank Amber was in, realizing it was too late to resuscitate her, a new wave of tears coursing down his face.

"Professor, I'm sorry, I tried to convince him to start it back up," Tyson spoke softly, seeing how broken the man looked.

For some reason it was oddly familiar, even seeing the fetus, it was as if he knew about this, but couldn't place it.

"I failed him, I failed him," Sebastian sobbed, a near animalistic scream tearing out of his throat.

Worried about the other two clones, one of the others grabbed the brunette, asking him to take the professor to his room. Until he calmed down, his emotions could prove hazardous to the clones' emotional and mental development.

Understanding, he easily scooped the smaller man up, carrying him to the room, told where it was.

He ignored the other's thrashing and kicking, the fists pounding into his chest and back when having to adjust carrying him.

Reaching there and as gently as he could, putting him in the bed, Tyson stayed with the scientist.

He took a seat, staring at the other, unsure if what he was seeing was real, the man so broken, crying loudly into the pillows.

He continued screaming about his failure, about his promise broken.

Hearing him like this, seeing him so hysterical, the Rocket felt a pain in his chest, as if he knew exactly why.

But why?

Why would he feel so horrible about this?

Why did this feel so familiar?

The pain? The sorrow? Feeling helpless…

At some point, the distraught man had cried himself to sleep, the brunette plucking the glasses off his face and setting them on the nightstand.

"What happened to you?" he asked, unable to resist brushing the tears off the other's face.

* * *

 _ **Not easy to write, and I'm happy/not happy with how it turned out, mostly with how short it is compared to some of the other chapters.**_

 _ **But yeah, more emotional/psychological stuff, and most of all, Giovanni being a total dick. Not sure if the money excuse could work, may switch it from money to time, or use a combination of both.**_

 _ **Either way, a new low for Giovanni and another reason for Professor Sebastian to hate him.**_

 _ **Advice to lengthen it, or take pieces out to put into the previous chapter, the rest into the next would be great.**_

 _ **Please read and review**_


	9. Chapter 9

It had been weeks since it happened, the destroyed life slowly rotting away in the tank for all to see.

Many have tried to wash it out, yet the emotional pain was too much, unable to go near, not even to try covering it.

Even Sebastian, one many would expect to handle such a difficult chore couldn't even do it. He wasn't able to bring himself to face the reality that the last thing connecting him to Fuji was gone.

The thought alone made him sick, his hatred for Giovanni building to the point he would be bedridden, his emotions becoming too much.

Tyson stayed, having been ordered in case the professor decided to go through with his threat to destroy the twins.

But he knew the other wouldn't, he could see it in his eyes, he cares too much about these Pokémon. It had been merely a bluff to try and dissuade Giovanni from killing the third clone, but it had failed.

He never felt such anger at his boss, how callous he was to just flip that switch, destroying the life inside.

Team Rocket has killed before, but seeing _this_ , it made him sick.

Giovanni is stepping out of bounds, _way_ out of bounds. If his mother was around still, she would've set that damn bastard straight!

She would never allow it, even if it cost her money, she would've found a way to make that money back. As Sebastian said, that child would've been the first successful human clone. A lot of money would've been earned with that kind of success, especially in the black market.

Speaking of the ingenious professor, he found him in his room, a bottle of whiskey lying by his side.

Angered that he'd take up drinking on the job, he snatched the nearly empty bottle away. He nearly jumped though when the other began to talk numbly, unsure if he even knew someone was present.

"Why do I get this rotten luck?" Sebastian asked, gazing at the wall, almost not entirely there, worrying the younger man.

"Professor…"

"Don't call me that… You _really_ don't remember, do you? You don't remember _him_ at all?" he asked, turning to face the younger man, his face hard to read.

It was in anguish, that much was obvious, but there were so many other emotions swirling about, it was hard to tell what he was feeling exactly.

"What?"

"Do you know _how_ we got to know each other?"

"I…"

How _did_ they get to know one another?

It wasn't through a job, it was something else, _someone_ else that brought them together, to become friends.

"I…I can't remember, it's a fog," he admitted, ashamed of his answer, seeing a bitter smile on his face.

"I wish I was like that, maybe then I wouldn't be like this."

"What happened here?"

"It wasn't here, it was Mewtwo."

"The clones?"

"No, the original clone. There was one before them."

"How? How do you know that?"

"I saw him after he destroyed the lab, killed people, killed the man who brought us together as friends."

"Why didn't you _say_ anything?"

"I don't know, maybe if I had, I could've saved Amber. But I forgot, silly huh? I didn't get my memory wiped, but at that moment, I forgot."

Tyson was speechless, not knowing what to say to the other, seeing him so depressed, the smile not reassuring him.

Was there a chance he may _actually_ commit suicide?

Possibly take the clones down with him, either to save them or get back at Giovanni for killing that human clone?

"You're going to report this to Giovanni, aren't you? Tell him my team and I kept this _big_ secret from everyone. We're probably the only ones who know about Mewtwo; know how we came across the DNA. The team that worked on Mewtwo, the man who got me part of this project."

"Thomas Fuji…" Tyson gasped, the memories flooding back, almost painful, everything in a jumble, struggling to try and put it together.

"You remember?"

Sebastian looked over, seeing the man clutching his head with one hand, taking deep breaths to keep himself from passing out.

Once the room stopped spinning, he gave the other a mournful look, enough for the other to know he remembered.

The other felt tears beginning to form as memories of them and Fuji out in bars or at headquarters, having fun, talking him into cutting loose.

"You were raped, I helped cover for you two so you can get looked at," he whispered, the other cringing having _that_ memory brought up. "I covered you before, I'll cover you again."

Realizing what he meant, the scientist stared at the brunette, eyes wide, unsure if he heard him correctly.

"If Giovanni finds out…"

"He won't, I'm the only one here. I told him I could watch you, keep you and your team out of trouble."

"Th-thank you…"

"Shiranui, I know you've been trying to take care of Amber's body. I think I have an idea how to pay respect to her."

"What?"

"Remember what Tom said he did for her?"

Recalling the words, how the tale was repeated when Tyson was curious of Fuji's involvement in Team Rocket.

"Cremation…"

Nodding, he saw the other give a bitter smile, slowly getting out of bed.

"We can hold a small service, the least we can do for her. We can even perform one for him too. They _both_ deserve it."

"Yes…" he sighed before a thought crossed his mind. "Tyson, do you believe in an afterlife?"

"Hmm?"

"Do you?"

"I guess so; it never really crossed my mind. Why do you ask?"

"Thomas told me he was able to bring her consciousness back, that she'd remember everything up to her death. If that is true, what would her reaction be to finding out her father's gone? That he died at the hands of something he was made to create _just_ to bring her back?"

"Put it that way, she would be pretty upset…"

"Exactly, maybe in a cruel twist of fate, it's better this way. Thomas wanted to reunite with his child. If there truly _is_ an afterlife, they may already _be_ reunited."

"And if that's the case, she could've been pulled away, brought back to the living, possibly recalling or something?"

"Maybe… I never really focused much on spirits. No one in my family was religious. You could say I'm pretty ignorant to it."

"I don't think so. You made pretty good points so far," Tyson reassured, placing a gentle hand on the other's shoulder.

"Guess I have."

Going down the halls, Tyson offered to collect everyone and if willing to wait a day or two, get proper clothing to wear.

Thanking him, he got to work in finally draining the tank, storing it into a more portable one and placing it into the freezer.

Whatever there was of her was too tiny and degraded, it was easier to freeze it all and crush it into a fine powder to scatter.

Within four days, things were set, everyone dressed in formal wear, Attila and Hun called to join, knowing the latter would've wanted to join.

Gathered together, the night gracefully cool to avoid the frozen powder melting right away, they stood near a lake, one Sebastian felt was suitable.

The forest was so beautiful, peaceful even, the sky clear for stars to shine, the wild Pokémon roaming about making minimal noise. It was as if they _knew_ what they were doing, curious or willing to mourn from afar.

They each shared words, most of them regarding Fuji, how great a man he was, the heart he had, the love he shared for his daughter.

When it came to Sebastian's turn, he nearly choked, managing to make his own little speech, ironically being the most impacting.

He spoke similar words, yet they were deeper, others putting it together just how precious the deceased man had been to him. The type of bond he had for him was far greater than any of them would have suspected.

The love he held for him immense, seeing it from how broken he was of Fuji's passing, living with the regret of never telling him his feelings, losing Amber.

By the time he finished, nearly everyone was in tears, those normally holding stoic appearances feeling their eyes burning, barely holding back the waves. Others not as emotionally stable broke down, sobbing into hands or someone's shoulder and chest.

Once everyone had calmed somewhat, the powdery remains set to be scattered, Tyson taking care of task, seeing his two friends were too distraught.

For once, they _actually_ felt human, even Attila moved by this, having never seen his partner so emotional.

Watching the powder float away, some landing in the water to become one with it, the rest caught in the wind, carried off to as far as they would go.

The sight was disturbingly beautiful, sounds of sobs still heard, most coming from Cassie, her face buried into Davin's chest.

As they returned to the lab, the two agents were convinced to stay for the remainder of the night. They were tired, it was obvious, so they agreed, choosing to leave when the sun rises to resume their search for a Key Stone.

As they came in, Sebastian decided to show the two the sleeping clones, both in awe at the sight.

"They're beautiful," Hun whispered before he could stop himself.

"They're the fruits of mine and my team's labor, of Thomas' labor even. If he had never found them, _they_ wouldn't be here, _I_ wouldn't be here, _none_ of us would be here right now. We may never have become friends, merely saw one another as coworkers, maybe as pawns."

"In some ways, this project brought us all together, one way or another," the silver haired man spoke as he gingerly brushed his hand along the tank.

"Do you think they're dreaming?" Attila asked as he saw how innocent his partner looked, unable to suppress a thin smile.

"I can't be for certain, maybe they are, maybe they're not. Unlike with Amber, when Thomas tried, when _I_ tried to bring her back, no attempt to bring their consciousness back was ever made."

"So either they're minds are completely blank, or they may be dreaming of their previous life?" the blonde wondered.

"It might simply be something we may never know," Sebastian spoke as he showed them their spare rooms.

"Pro…Shiranui, if you need anything, call us," Hun spoke, turning to his friend with a thin smile. "We'll help you with whatever you need regarding them."

"I appreciate it, I really do," he smiled as they eventually parted ways to sleep.

When he lied down, he looked up at the ceiling; eyes slowly closing, for the first time in a long while, the nightmares were kept at bay.

* * *

 _ **Little easier to write, but not as happy with how it came out, length wise mostly.**_

 _ **I was going to have this and Chapter 8 as one, but I couldn't find a way to meld them together or something.**_

 _ **Any advice on how I could lengthen this chapter or possibly take pieces to put into the previous/next chapter would be great.**_

 _ **Please read and review**_


	10. Chapter 10

Some weeks after the duo returned to Kalos, Sebastian devoted much of his time relating to the twins.

Between taking notes, he already began making plans on how to help them adjust to their new life.

They were still small, but much bigger than before, obviously grown enough to survive outside their tanks if he were to release them now.

He only delayed it for the sake of their immune systems to develop a bit more, having injections given to them to insure it happens.

Once they were stable, he would plan on waking them up…

But much to his annoyance, Giovanni _still_ kept returning, wanting to see their progress, refusing to leave until he gets what he wants.

"How dangerous will they be?"

"I can't be certain, even when they're out, they'll be far too young to do _any_ form of battling. I've been putting together exercises to teach them how to move about, develop their muscles and basic psychic control."

"And to be battle ready?"

" _That_ could take months, maybe a year before they would be ready. Their bodies are completely unknown. I would need to test them, to make sure they have the strength to handle it. If they can't, it would be like throwing them to a pack of Mightyena!"

"If they cannot fight, then it would be best to destroy them, take their DNA and try again, but faster."

"Are you _insane_? I'm not going to destroy them like that!"

"You were before when I pulled the plug on your side project."

Sebastian froze, recalling those words, looking away, hearing the man laughing at being cornered.

"I was under a lot of stress…"

"I'm _sure_ you were," he taunted, the same grin never leaving his face. "If need be, you could always dissect one now while the other's still growing."

Glaring at the floor, he listened to the other leave, taking a deep breath, hissing through his teeth.

"Bastard…"

After those strangely chilling words, everyone began to feel anxious, unsure if it was nerves or something else.

It made matters worse when Tyson was made to return to headquarters, therefore if something _were_ to happen, they were nearly defenseless. Only a handful of them carried Pokémon, but whether it'd be enough or not, they weren't certain.

As they started to get things packed in for the night, sleep needed greatly, Sebastian gave the sleeping clones a soft smile.

For some reason, they helped relax him, seeing their peaceful faces.

"Sleep well Beta, Omega."

After talking with Attila and Hun about whether or not the clones might've been dreaming, he decided to start talking to them. With some, it might've looked silly, but it felt oddly comforting, as if they _were_ listening to his every word.

He apologized for disappearing so much, promising to be there when they're born, that he'd help them learn whatever they want.

He made various promises, some he wasn't sure he'd be able to keep, but saying them made it feel true. If not right now, it would happen soon enough, something he would always say, reassuring them and himself.

Lying in bed, he was burrowed deep in the blankets, bittersweet dreams of Fuji standing there, waving and smiling at him. By his side was the little girl from the photo, the little girl whose father tried to bring back…

Amber…

They were so happy, as if thanking him, but for what?

He wanted to ask, but before he could, the world vanished, replaced with the white walls of his room.

He blinked, seeing semi blurred faces, shouts echoing around him.

"Shiranui, wake up! There's something wrong with Beta!" Cassie shouted, shaking the man awake, face filled with panic.

"What happened?" he asked, grabbing his glasses, forgoing with dressing as he followed her in his pajamas.

"I don't know, she was like this when Davin went to check on her. Joel and a couple others are checking the security tapes right now."

As she explained, they came into the room, seeing bodies running about, trying to find the cause as the mentioned clone's heartrate continued rising.

"Have you given her anything?"

"No… I mean we tried sedatives to calm her down, but nothing's working."

"That bastard," Sebastian growled, having a faint idea who's to blame. "Get her out of there now! We'll have a better chance to save her."

Nodding, they began putting in the commands to drain the fluid and open the tank, ready to grab her.

"They aren't working!"

"Get out of the way!"

Sebastian shoved one of the scientists aside, his actions reasonable as he worked the keys, cursing when realizing that the codes and passwords had been changed.

"Damn you, Giovanni!" he found himself snarling.

Turning towards the tank, he felt bitter tears forming, realizing he was going to lose another life.

And like before, there wasn't a damn thing he could do about it!

The glass was too strong; he wouldn't be able to break it open with physical force.

"Beta…" he whispered, feeling completely helpless, wishing something would happen, _think_ of something to save her.

A series of crunching like sounds were heard, everyone freezing, staring at the tanks when locating the source.

They could see cracks forming, a bluish glow enveloped around Omega.

Her eyes were cracked open, a blue glow coming from them, revealing she has gained consciousness, possibly due to Beta's suffering.

Slowly, the glow died down, the weight of the water pushing the glass apart, watching as it fell in a heap, both Pokémon freed.

Sebastian stood there, not believing what he was seeing, ignoring how the cold water flooded past his bare feet.

He came out of his stupor when hearing the suffering psychic hacking and coughing, loud wails escaping as she took her first breath.

Not long after, the other one began crying just as loudly.

Both of their eyes were squeezed shut, their voices growing louder as they shivered in the cold.

Before he could stop himself, he walked over, eyes still wide at what he was seeing, _hearing_ in front of him.

He ignored the worried voices of his team, his friends, the glass crunching and imbedding into his feet.

The noises they made, the crying they were making, it reminded him of when his daughters were first born. That day was fresh in his mind, forever imprinted much like how this day will be.

A swell of joy, pride, and most of all relief swept through him as he reached the pair, grateful the tanks were near one another.

With near grace, he wrapped his arms around them both, gently pulling them close, cradling the two.

They were much bigger than an infant, but small enough to hold both with relative ease, the action enough to stop their cries.

"You don't have to be afraid now. You're both safe now," Sebastian comforted, keeping his voice low so not to frighten them.

They looked at him in wonder, large puffy eyes, fur still damp, their faces wetter from their tears.

"You're both okay," he sighed, relieved as he stepped away, slumping into a chair, refusing to let the little ones ago.

They each sat on his knees, their cries long gone, now replaced with curiosity as they began to poke and prod the being holding them.

Their small paws tugged and poked his pajama top, sniffing him, taking in his scent as well as each other.

Sensing no harm, they burrowed in, the cold returning, making him hug them closer, letting them take as much warmth as they need.

Looking up at his team, seeing their stunned faces, relief and worry showing, he understood why. What he did was risky getting near them, knowing they could've attacked out of fear, but they hadn't.

Deep down, he _knew_ they wouldn't attack. They were scared, reacting on instinct, _still_ following that same instinct.

"Davin, get some towels. Joel, you and the others clean this up and collect what you can of the water. Something _had_ to have been put in it or the tubes. It's clear she couldn't breathe, but from what…"

"We'll figure it out," Cassie reassured, as they all got to work on their given tasks.

Feeling paws now at his face, examining the skin, the goatee, the stripe in his hair, glasses he wore.

A small laugh escaped as one made a swipe for his frames, attempting to peer through them before he took them back.

"Now, now, these aren't for playing," he gently scolded, the loving smile never leaving his face.

"Mew?" Beta chirped softly, the first noise to make aside crying.

Sniffing his hair some more, she grew curious as she gave the stripe a lick, making a confused face at the taste as her tongue hung out.

He couldn't hold back a laugh, not realizing a few tears fell from his eyes, loving how innocent and playful they are.

As the mess was cleaned, two of scientists stepped away from cleaning, wanting to examine the clones.

Sebastian agreed, knowing it had to be done, despite how much he wanted to continue holding them, knowing they'll get scared again. But it was for the best, reassuring them that they'll be back when they started to cry.

As if understanding, they settled, getting distracted by the scientists now holding them, pawing at them much like they had with him.

Just as he began to relax, he jumped when his foot was grabbed, pain registering, hissing through his teeth.

"Sorry, Shiranui," Cassie apologized as she brought a stool under his feet, propping them up. "That _was_ pretty dumb what you did, but at least they're okay."

"I know, I don't know what came over me. When they started crying, it felt like I was back in the delivery room. My daughters just born, Meiya out cold from the labor, the girls crying away. The second I held them, they stopped, as if they _knew_ who I was, that I wasn't going to hurt them."

"You really miss your daughters, don't you?"

"I do, I haven't seen them in so long now. Between jobs Giovanni puts me through and Meiya snatching them and taking them to Arceus knows where, I never got to hold them again. It hurt so much losing them like that; it was like a part of me died. If I could go back in time, I would've made sure _I_ was the one to take them. I would've cared for them the way they should."

"What about your ex-wife?" she asked, knowing it was touchy, but had to keep him somewhat busy.

There was a lot of glass, some of it buried pretty deep, sizes all over the place, and it was both feet too. It was going to be a lot of work and _a lot_ of stitches.

Hopefully, there wasn't any permanent damage…

"As much as I hate her now, I would let them see her. She _did_ give birth and maybe has _some_ love for them. But, if she _honestly_ doesn't care, then I won't let them near her, risk her poisoning their minds."

"It must be tough."

"It is, especially now that Giovanni's using them as leverage."

"Oh…"

After that it was silent, the other cringing or making hissing noises as his feet were treated, stitches and bandages covering them.

It was almost impossible to walk, needing help to move before giving up, sticking with a wheel chair until he recovered.

But as the days turned to weeks, the clones showing no adverse signs to their health, he was content to be stuck in the chair.

It simply meant more time for them to hop into his arms, wanting to be held, their more feline instincts showing. It was more prominent by how they walked on all fours than using two legs as Mewtwo had done. That and they would start purring or occasionally let out a hiss if they nipped themselves or each other.

Their curiosity was noticeable, watching with a smile as would others when they'd explore the lab or the play area they set up for them.

He watched as Omega would explore, sitting on her haunches, attempting to peek over tables or shelves to see.

Sometimes she would reach out and swipe something, mostly a pen or some sheets of paper, batting them around.

Beta though was more disastrous with her explorations, making leaps onto the tables, knocking things over with her clumsy body.

One time she had knocked over a bottle of ink, almost consuming it if he hadn't called out to her. The look on her face was priceless, her paw almost to her mouth, ink on one of her fingers to taste it as he wheeled over.

He never struck them if they were overly mischievous; he had to be careful not to upset them too much. But he couldn't risk letting them be spoiled either, grateful they somehow could tell when to stop by his tone.

He knew which clone was which, making it obvious whenever one of the others had trouble doing so.

"How are you able to tell that this is Beta?" one of the scientists asked, clearly confused as Sebastian gently groomed said clone after a bath.

"When their eyes are open, Beta's is a dark, almost plum violet while Omega's is a frosty lilac. While both their coats are lighter than Mewtwo's, Omega's is a _little_ darker, particularly her tail. And most importantly, if you get them to hold still long enough, you'd notice Beta is a little bigger than Omega," Sebastian laughed as the small psychic purred at the attention.

"I don't think I would be able to pay attention long enough to pick those details. That and they move around so much," the other laughed as he gently scratched the psychic behind the ear.

"They _are_ babies and it's good for them to explore. They're learning, and so long as we watch them, they'll learn what's okay to touch and what isn't."

"Like that bottle of ink?"

"Yes."

Within a couple more weeks, Sebastian began walking, albeit a bit stiffly, his feet still tender, but far better than before.

One of the many reasons he loves science so much, the medicine developed has done so much. Because of it, injuries like these last only a week or two than months, possibly a year depending on how bad they are.

Gently, the bespectacled scientist ushered the two into the play area, wanting to help them learn more.

When they were inside, he sat down, wanting to involve himself more with the games he has set up as well as give his feet as much rest as necessary.

"See this?" he asked, watching as they both listened, staring at a blue ball. "I'm going to put it in this cup and move it around with others. When I finish, you'll take turns picking out which one it's hiding under. If you find it, you get a prize."

"Mew!" Beta purred, tail wagging happily.

Both watched, trying to follow as he quickly scrambled the seven cups, making sure not to knock one over.

If they had been something else, he would've gone much easier, but they aren't normal, knowing they're intelligent despite their actions.

When he finished, he gave them a smile, seeing them stare before Omega nudged her sister to go first.

That was something else he wanted them to learn, taking turns, sharing things together, something they both seemed to grasp easily.

Not only would it help them get along better and possibly other Pokémon they may meet, but when they do start to battle. They would need to know not to get impatient, learn how to read their movements to know how to react.

Hesitantly, Beta eyed the cups before picking the one furthest from the rest, smiling as the small toy was revealed.

"Mew!"

"Excellent job," he laughed, pulling something from behind himself, revealing some snacks Joel had made. "Pick whichever you want."

Smiling happily, the older twin snatched up what she wanted, watching as he put the rest away.

Repeating the process, making sure the ball was somewhere else, though by how fast he moved for Omega, he nearly lost track.

As before, the younger one found it, rewarding her with a treat as well, watching as they both ate happily.

It was like this for a while, using various games like these to test their memory and intelligence.

Other games worked on their motor skills, working with blocks to match with various objects, showing them puzzles.

He noticed they each had a preference for certain games he and the others set up for them both.

Beta enjoyed ones she could get her paws on, particularly the more physical games to tussle around with. Omega on the other hand preferred ones to test her mind, playing with various puzzles, finishing some fast, others taking longer.

Slowly he started to make them harder, not so much new games, but _how_ to play them, such as working on their psychic control.

He asked for someone to bring out a psychic to show them what it does, knowing a demonstration is the best method for any child to learn.

Once they started, he noticed how much more fun they were having, Beta using hers to bring things off of shelves she couldn't reach to play with.

Omega would do the same to retrieve a favorite puzzle or picture book, using the same psychic control to enjoy her time.

Doing this, they were beginning to be more independent and thinking things through to solve certain problems.

The idea was risky, knowing Giovanni wouldn't entirely approve, but since they're still young, they can still be molded.

At least that's what he'll tell the bastard to shut him up.

"I think we can take another step," he smiled, knowing he needed to broaden their senses and horizons.

"What are you going to do?" Joel asked as he helped set down the clone's lunch, albeit they retrieved them faster with their abilities.

"Take them outside. They can only learn so much in here before they get bored and restless. They could learn to climb trees and swim in the lake, strengthening their muscles. Use their psychic control to move things about, things that would be heavier than here, which they're allowed to move."

"Are you sure that's wise? What if a trainer shows up?"

"Use your Kadabra to knock them out with Hypnosis and wipe their memories of ever seeing them. _If_ they even saw them to begin with."

"Right," he nodded with a smile as he sat down next to his senior. "When are you thinking of bringing them outdoors?"

"Tomorrow, it's supposed to be sunny out, and we had some rain, but not enough to be concerned over."

"I guess we should also prepare for baths? I'm sure they're going to have _a lot_ of fun splashing in the mud."

"Right, I forgot about that."

* * *

 _ **Please read and review**_


	11. Chapter 11

Just as promised, Sebastian brought the two outdoors, the pair slowly working on walking on their hind legs.

They weren't taught to do so; they just started to do so than relying on all fours.

It was obvious that they were copying them, _him_ mostly by how they always followed the professor just about everywhere.

He even let them curl up in his bed, having extras made for when they began to get to big, but while little, he'll be willing to spoil them with sharing a bed.

Seeing how they lit up, seeing the sky for real, not just through a window, the fresh smell of grass and dirt. Even _he_ almost forgot about it, enjoying the fresh air himself, fresher from the previous rain.

He showed them the lake, letting them test the water, lapping at it when thirsty, bat at their reflections.

"Don't wander out to far," Sebastian warned, watching as they chased each other in the shore, water splashing about.

"You're sounding like their father," Joel teased as he sat down with the other, his Kadabra relaxing in a tree.

"They're babies, _someone's_ gotta watch over them."

"I know, at least you're not overprotective."

"It wouldn't be fair… That and…"

"Giovanni?"

"Yeah, I know he'll take them and I'm scared. I don't want them to suffer. I rather see them like this. Innocent and playful."

"Why _did_ you start working for Team Rocket? Just between us."

"I was young and stupid. I didn't know what I was getting into at the time."

"But you stayed."

"Because of my daughters, I stayed in hopes I'd see them. I was willing to do _anything_ to see them again. I'm not innocent, I know that. I know that when I die, I'll probably burn in Hell or whatever place exists for people like me. I've done a lot of things in my life, things I didn't regret, things I _now_ regret."

"You know, in Kalos, they have small religious sects. I was part of one before I started working for Professor Sycamore as his apprentice, before I traveled to Kanto, before joining Team Rocket, _your_ team specifically."

"Hmm?"

"Each one is unique, following certain creation deities, each one having something that made people feel safe and secure."

"What were they?" Sebastian asked, his curiosity grabbed by this.

He couldn't help but recall the conversation he had with Tyson about the existence of an afterlife.

And now to find out one of his _own_ scientists is religious? Something inside him told him this was more than a mere coincidence.

"Well, the main one, one most follows, some following it and some other because of the similarities is Arceus."

"That makes sense, far as I recall, Arceus did create our world from various studies. It even created worlds for other deity Pokémon and other kinds similar to them."

"That's exactly correct. Most follow Arceus by following the example of appreciating the life we were given. To appreciate the gift of being able to choose what we want, how we feel, how we think even. Some even worship the Lake Trio for the same thing, but more on what they represent."

"I doubt it's that easy though?"

"No, not only do they worship him to appreciate the life given, but know when it is right to forgive someone for their wrong doings. If someone stole something to help another, they would be forgiven easier than if they stole out of pure greed. Some are less forgiving to those who wrong others, who wrong Arceus' creations, be it human, Pokémon, animal, anything."

"Put it that way, I know _I'm_ not on its favorite list then," the man joked dryly, letting the other continue as he watched the playful clones.

"With those who worship Arceus, in some ways its judgement would be harshest which is understandable given its status and such. But remember, there _are_ others who helped with the creation of what we know too. Pokémon with nearly the same power and strength as Arceus itself," Joel pointed out with a playful wag of his finger, seeing the other cast him a light scowl.

"So what do the others represent then?"

"With Girantina, those who worship it are those who see it as a guide for lost souls, both living and dead. It forgives those who are lost, unsure where they belong, having been viewed as outcasts as it has been. Because of Girantina's power, from the tales told of it, it had been banished to its own world, rarely venturing out through tears that appear or it made. Everyone simply wants to belong, to feel accepted, to have friends and family who appreciate and love them for who they are."

"How does it fare in the forgiving department?"

"From what I had read about it, it is said that Girantina is more willing to forgive people who did wrong, but out of desperation. If they had no one to guide them much like itself, it's only natural they'd act out. Sometimes…sometimes you simply _have_ to do something that is considered wrong to survive because there's simply no other way."

"I see…"

"Those who follow Dialga are those who appreciate the time they are given alive, from the day we're born to the day we die. People who worship it neither rush to live life to its fullest, but don't trudge slowly. They simply got at a pace they're most comfortable with in order to enjoy life, whether they miss things or get to see it all."

"How does it judge people?"

"It is said that Dialga doesn't judge people while they're alive. It merely watches and once they're close to death or they have died, _that_ is when it will begin its judgment over that person. If they've done nothing but good deeds, obviously they'll be spared. If they done nothing but malicious things with no regret…"

"They'll be punished."

"And those who _have_ done bad things, but later repented now out of selfishness but regret, Dialga is more likely to forgive them. It'll also forgive those who did what people consider evil deeds, but it was out of their control. They could have been forced to in order to save loved ones, fallen ill that hinders their own judgment. Same with those who honestly believe they're doing good, but have gone about it the wrong way."

"That's an interesting take. What of Palkia though?"

"Palkia's a bit strange, it's a bit of both Girantina's method and Dialga's mixed together. Maybe because it controls space than controlling something like distortion or time as they do? What I _can_ remember, being that it controls space, people who worship it are those who are more of appreciating the _sort_ of life they have."

"How so?"

"You've heard how Palkia likely is capable if not _has_ created alternate realities from this one, right?"

"I have… I think I get it. What these alternate realities could consist is unknown. There could be another you who could be worse off than you. They could be rich and lonely, poor, a slave, anything that is a complete opposite of yourself."

"Exactly, and at the same time they believe that Palkia, next to Arceus is what gives people the reason to exist. While Arceus created everything, Palkia stabilizes it so we have the chance to use Arceus' gift. But with that, Palkia is rather neutral about judging others, only going after those that are deemed a real threat to punish them."

"Quite fascinating. I'm sort of regretting having never taken any classes to learn about them when I was in college," Sebastian chuckled softly. "If I may ask, which one of them do you follow?"

"Dialga, I just feel more at home, reading scriptures or making prayers and offerings to it."

"Offerings?"

"They aren't necessary; it's mostly done with small children to teach them how to show compassion by making an offering. It's mostly food related like sweetcakes or hot dumplings. They're mostly done during certain festivities that relate to the proper deity or all of them depending what day they fall to overlap or is one made for all."

"But I presume that the offerings aren't so much given to the deities themselves, but more so wild Pokémon struggling for food could eat?"

"Correct, especially in the winter season where food is scarce to begin with."

"Rather clever."

"It is, though I wouldn't be surprised if they did at times eat some of the offerings out of curtesy," the man laughed, making the other unable to suppress a chuckle.

"Joel?" Sebastian asked, turning to him, his face torn between being serious and looking scared. "Do you think Dialga would forgive me? Or any of them for that matter?"

"I can't say really… With Dialga, it won't judge you until you've died and in a sense tallies up your life. If you were to continue hurting others with no regret, it won't forgive, but because of your predicament, it _may_ forgive you. Especially with your recent actions. You tried to bring Amber back for Thomas, to fulfill his promise. You participated in the funeral we held for her and him. And let's not forget with the way you've been treating the twins since they woke up."

"And the others?"

"Palkia may in a sense ignore you, not deeming you threatening to life, especially if you're wanting, _have_ been protecting Beta and Omega. Girantina would likely forgive you because your actions are not all that willing, especially of late. As for Arceus, I can't say, it _could_ forgive for the same reason or simply punish you. In the end, it's _their_ decision, not ours to make."

"I guess you're right," Sebastian sighed glumly, drawing his knees up, his chin resting on top.

Part of him wished he hadn't asked, his excitement for learning disappearing when thinking about it.

Joel silently understood, saying nothing more, letting silence rest comfortably between them.

Both men sat together, tension ebbing away as they watched the clones continue playing together in the water.

After a while, they grew bored, wanting to visit their creator, their _father_ as the younger scientist and others would joke.

With mewls and chirping, Sebastian couldn't help but smile as he let them climb all over to snuggle into his arms.

He ignored their wet fur, how soaked, muddy even his clothes are going to get.

"Having fun, you two?" he asked, feeling better now that his attention rested on them than his own weary mind.

As they spent some more outdoors, the sun began to set, signaling they should return to the lab before it grew to dark. It would be dinner soon and the clones, the adults even, needed a bath before eating.

Each psychic clung to Sebastian's hands, eager to walk, thankfully not taking long to return to the familiar building.

Getting them inside, he, with Joel's help, got them and themselves cleaned up, eating shortly after, the remainder of their time spent with the clones playing.

Beta was easily amused by the familiar toys, currently wrestling with a large plush, tail thumping about as she pounce and thrash around.

Omega on the other hand was staring intently, obviously fascinated with the blocks she pulled out.

Walking over, Sebastian knelt down next to her, seeing her focus now brought upon him than the blocks.

"Mew?"

"Is something wrong?" he asked, unsure what could be wrong. "We can go back outside tomorrow if you wanted to play some more. I promise."

Shaking her head, Omega pointed towards the blocks, then to his amazement, used her psychic ability to claim a book one of the others were reading.

It didn't take him long to figure out what she wanted, unable to suppress a smile at her eagerness to learn something entirely new.

"You want to learn how to read? I'll be happy to teach you."

"Mew!"

Taking it as a yes by how happy she looked, he pulled out more blocks, setting them up to show all the letters of the alphabet.

"There are twenty-six letters; each one is unique and different. When you put them together, they make words, the very things we read and speak. Even alone, they have a purpose when used correctly."

Despite being so young, he knew Omega was far more intuitive, picking things up far easier than her sister.

Part of him wondered if in the duration Beta had suffocated, she ended up with some mild brain damage. It would explain some of her more childish antics despite how much they've been growing now.

Sadly, they never found what was in the fluid or anything noticeable in the tubes that had been inserted in her and Omega to feed and help them breathe.

The closest they got was a disguised being teleporting into the lab with an unfamiliar psychic type and rewriting the programing.

Whatever else he did, they were at a loss and it frustrated them all, the head scientist most of all.

Shaking that thought out, while they would continue to try and figure out what happened exactly, he was just grateful _both_ were alive. Both of them were alive, healthy, and happy. That was enough to leave him content for now.

He told her more about the letters, reading each one out for her up until he saw her yawning, knowing it was time for bed.

Beta was already passed out, face burrowed into the large plush she was _"_ _sparring"_ with, soft snores heard.

Picking them up, he brought them to their room, letting them sit on the bed as he left to wash up and change for the night.

Returning, he was able to maneuver around the two, Beta partially awake as she and Omega clamored all over him to get comfortable.

Settled, they all fell instantly to sleep, letting the events of the day fill their dreams before the sun rose once more.

The routine was nearly the same, yet kept different, especially when it came to the clones going outdoors, playing about in trees or the water.

They slowly began to learn how to swim, Sebastian standing in the deeper water so they could hold onto him in case they panicked.

Despite having feline traits, they absolutely loved going into the lake, splashing in the water, slowly paddling about.

When they eventually returned indoors for lunch, the scientist having thrown some loose sweats and a T-shirt on to avoid getting a chill, he felt his breath hitch.

Barely passing one of the labs, Giovanni stood, having apparently been waiting, a sour look on his face.

"Is there something wrong?" Sebastian asked, unknowingly pushing the two behind him, the pair staring at him worriedly.

"I came to see how the clones were doing and find you _and_ them missing. Care to explain yourself?" the boss asked in a tone that sounded _to_ calm for the other's liking.

He knew the man had taken note he was wet, hair still dripping, even the clones still somewhat damp.

"I was teaching them how to swim. It would've been beneficial to their growth, _especially_ when it was time for them to learn how to battle," Sebastian answered, knowing it was true.

"Why would they _want_ to learn how to swim?"

"If they were to get into a confrontation that led them being over water, they have a higher chance in surviving. Something could happen where they may not able to use their telepathic abilities to stay afloat. They would be able to last longer in the water to continue defending themselves or swim back to shore."

"I'll give you credit on that, it makes sense. But that doesn't explain why _you're_ wet," the other replied, arms crossed behind him as he studied the other.

"They _need_ someone to hold onto while they adjust before making _any_ attempts on their own. They're only babies, their muscles are still developing."

"Aside from that, how _have_ they done? Are they possibly ready for any battling?"

He resisted the urge to snap at the crime lord, not wanting to upset the clones any more than they may already be.

"Not yet, they're far too young for any form of battling. The closest we get is when they tussle around with each other or toys we've set up for their exercises."

" _Toys_?"

"I've set up a room you would think of as a playroom, but it has its uses. They're both young, and because of it, they would have a shorter attention span much like any normal child. They easily get bored, constantly having to keep them stimulated with various activities. It could go between working on puzzles, locating hidden objects we set about the room, tussling with large plushes or something firmer."

"So you've basically been wasting your time, theirs, _and_ mine goofing off?" the leader growled.

"Not at all," the other argued, gritting his teeth as he felt the psychics beginning to tremble at the other's growing anger. "These _games_ have been stimulating them. They're learning how things work, learning how to use their psychic abilities. If it hadn't been done so, they would likely have destroyed something or someone, maybe even themselves inadvertently."

"Start teaching them how to fight."

"Didn't you _just_ hear me? They aren't ready!"

Without warning, Giovanni's fist collided into the other's face, making him cry out as his nose began to bleed. He wasn't sure if it broke, he didn't hear it break, but that doesn't mean it wasn't.

The impact knocked him over, hearing his team crying out in fright when hearing the confrontation.

He could hear the clones beginning to wail loudly, scared and confused, upset to see him hurt, having never seen blood before.

"In case you've forgotten, _I'm_ in charge," the leader threatened as he knelt down, grabbing the front of the other's shirt. "I would highly suggest that you don't forget that in the future."

Shoving him back, he walked around him, his expensive shoes crunching the fallen frames, walking past the angered scientists and sobbing clones.

Once he was far enough away, the others rushed to their friend's aid, some getting tissue to help stop the bleeding.

"Damn him," Davin spat, glaring at the doorway the man went through. "Doesn't he have a heart?"

"If he did, he threw it away a long time ago," Sebastian groaned, trying to ignore how much his face now hurt.

He noticed that the clones were no longer crying, which had concerned him that they might've run away, not that he'd blame them.

He froze when a paw gently touched his face, the others having stepped back, seeing the small Pokémon reaching for him.

Being this close, he could recognize the familiar plum eyes, knowing it was Beta examining him.

With a faint glow, the pain suddenly began to disappear, recognizing the move as Heal Pulse, the Pokémon appearing to act on instinct using it.

Seeing a similar glow further off, yet different, curious of what Omega must be up to before seeing the blurred image of her walking over.

Feeling something drop in his lap, he found it was his glasses, realizing the younger clone had _somehow_ repaired them when holding them up.

He wasn't sure how it had been possible to do this, but for now, was willing to push it aside. He could always look into it later on.

Right now, he was in too much shock witnessing them using _actual_ moves.

Putting the repaired frames back on, he looked between the small clones, seeing how upset they were, forgetting the pain he had just been in.

He was far too proud over what they did, without a single order given or shown how it's done.

And yet, it made him worry, Giovanni's threat ringing in the back of his head.

The surprised look turned to a small frown, pulling the two close, feeling them cling to his shirt desperately.

They aren't ready; they're too young to fight…

"Shiranui?"

He didn't want to answer, continuing to hug the clones, trying not to lose control over his emotions. He can't, he _couldn't_ risk hurting them if they picked them up, picked up _all_ his negative feelings.

"If he's going to make them start battling, then why don't _we_ be the ones to start teaching? They can go slow, learn how to use their attacks on things like logs and rocks around here. It would be safest before battling Pokémon."

"He's right, and Kadabra can help them learn how to control their psychic abilities as well as ensure they don't lose complete control. I'm sure he could explain things better than we ever could," Joel added, kneeling next to the other.

"I suppose so, if we aren't the ones to teach them, Giovanni will _crush_ them," Sebastian sighed, burrowing his face into his creations' soft fur.

Hearing them talk some more, not paying much attention to what was being said, he looked at the two, seeing how they calmed down. Both were now staring at their surroundings, maybe seeing a shadow or curtain moving.

When they turned their attention to him, large innocent eyes staring, he felt tears threatening to form.

"Do you two want to learn how to battle?" he muttered softly, knowing he may not get answer.

Beta cocked her head to one side, obviously not understanding the question, smiling innocently as she burrowed her face into him, purring.

She probably assumed battling is a form of play.

If it was under normal circumstances, it would've been…

Omega on the other hand, she seemed to give him this quizzical look, appearing more focused on what he said.

Slowly, she nodded, the man somehow not all that surprised, she was a fast learner, having already begun reading books.

She probably knows what the word means, likely reading it in a dictionary or one of the other books on the shelves.

Maybe even Beta knows through her sister?

The two are often chattering together, talking in their own language, always helping each other.

"Alright then, but not today, it's been stressful enough for all of us. Plans need to be made to ensure no one gets hurt. We need to find out what you two are capable of and what you can learn."

* * *

 _ **Of course Giovanni** has **to come and ruin things, least the professor has his team for some support, knowing the clones won't be in any real danger for a little longer.**_

 _ **Wonder what sort of moves they may know? So far it seems one knows Heal Pulse, wonder which skill the other knows among others between them?**_

 ***NOTE:***

 _ **Regarding the religion thing, not trying to shove anything down anyone's throat, it just seemed like an interesting idea to throw in.**_

 _ **May still need some tweaking, so ideas are welcomed, especially for the Palkia one.**_

 _ **I think my fave though writing up has to be Dialga's, probably due to it being my favorite out of them.**_

 _ **I got the idea for it ironically from reading Nuzlockes that used it, most of it just mentioned, not really delved into, others as some focus.**_

 _ **Please read and review**_


	12. Chapter 12

"Alright, we'll start having you practice basic attacks," Sebastian explained.

The two clones watched him as he walked over to some logs Joel's Kadabra had set up, gently patting them.

"For now, I want you two to attack these with whatever comes to mind. Don't focus trying to break them or destroy them even, just attack. We can work on controlling the power or how much is needed before we go further."

Both were still unsure, the man turning to Joel, who gave a curt nod as he gave an order to his Kadabra.

"Use Ice Punch!"

"Ka!" the Pokémon cried out. "Dabra!"

Charging at one of the logs, its paw curled into a fist, a chunk of ice forming as it made contact with the log. Cracks formed along the surface of the wood, a small crater created with ice and frost reaching around.

"Impressive," Sebastian smiled, the other practically beaming as was his Pokémon from the compliment.

After a few minutes, the two studying what they had to attack, watching as the ice began to drip from the bright sun.

Just as Sebastian was about to ask them if they were okay, that they understood, he nearly jumped when Beta made the first move.

Her paw began glowing before it was enveloped in swirling, green like energy, slamming it into a log.

"That was Drain Punch," Joel muttered, obviously impressed.

Before long, Beta attacked with what seemed to come to her instinctively.

The others watched her go into a series of attacks, unsure if there was a repressed memory of her battling in her former life.

Either way, when she was finally done, they counted what she could use, those being Heal Pulse, Drain Punch, Psycho Cut, and Aura Sphere.

"She prefers a more direct assault than attacking from afar, rather unusual for a psychic type," Davin mused as Beta rested, eating some snacks Cassie set up.

"They aren't perfect, but she has potential as she practices controlling them," Sebastian added, recalling a few times the Aura Sphere had went off to soon. "Omega, it's your turn now whenever you're ready."

Nodding, seemingly having a better idea, she studied the logs once everyone was out of the way.

It was obvious she was trying to determine how to use her unknown powers, everyone watching in anticipation.

Before long, she raised her tiny paws in the air, starting to form a light blue ball, crackling with energy.

The sight alone scared the professor, making him jump to action, "Omega, no! Don't use that move!"

Stopping, she gave him a concerned look, the other shaking, "Mew?"

"It's okay, just don't use _that_ move okay? It's far too unpredictable. We don't want anyone getting hurt, right?"

"Mew!"

" _That_ was to close for comfort," he sighed, falling back into a sitting position, feeling the older clone climb into his lap.

"Nice save there, Shiranui. We may need to teach her something else that _isn't_ Future Sight. As you said, it's far too unpredictable, especially at her age," Joel half joked, relieved as well as he plopped down.

"Maybe, for now we'll see what else she can do."

Just as with her sister, she attacked the logs, revealing to know Psychic, what was _going_ to be Future Sight, Signal Beam, and Heal Pulse as well.

"Both seem to have very unique moves, sharing only one together," Davin muttered as he looked at the damage the logs took.

"Makes you think if they really _are_ sisters," Cassie laughed as she helped pass snacks to the tired clone.

"That would be rather ironic if they actually were," her fiancé laughed.

After a while, the clones began to get restless, wanting to play with their newfound abilities some more.

Understanding, they had them practice more, particularly those they had trouble with, though Omega was still forbidden to use Future Sight.

After a few weeks passed, their control grew, the younger twin eventually allowed to use the unpredictable attack.

The first time was somewhat disastrous, managing to strike down the log perfectly, but the shockwave sent everyone flying.

Thankfully no one had been seriously hurt, but better understanding; they found a more remote location, one with boulders.

They had her focus on those, everyone hiding behind the rest until the shockwaves were better controlled as was the attack itself.

Whenever she wasn't practicing Future Sight, she'd work on other moves, her sister then joining her side to work on her own attacks.

Eventually they moved onto actual battles, Joel using his Kadabra and a Zebstrika to battle them.

He kept the Pokémon from using too much strength, letting the twins adjust to the style of battle, Sebastian guiding them with orders.

It was like this for a while, the sparring going on, the twins coordinating their attacks to work with each other.

And after each spar, they'd both use Heal Pulse to heal not only each other, but the other Pokémon they battled against.

"That's enough for today," Sebastian called, the twins panting, obvious they were having fun, but grateful to stop for now. "You two did wonderful."

"Mew!" both purred, nuzzling against him as he and the others returned to the lab.

Seeing how tired they were, he picked them up, carrying them back than making them walk or asking the others.

Arriving at the lab, he decided to relax in the kitchen everyone ate in; knowing dinner would be made and served soon.

Both clones were asleep, clinging to the front of his coat, their small faces dirty from the day's events.

Deciding that a bath was in order, he gently woke them up, the pair following him to the washroom to clean up.

When they were clean, the smell of food prepared getting stronger, they were eager to fill their stomachs.

Yet they found themselves stopping, Giovanni once more making another unannounced visit to the lab.

"So sorry to show up during dinner," he taunted, hearing the clones softly growl as they hid behind their creator. "Any progress?"

"They _have_ begun training, but they still have a ways to go," Sebastian found himself growling, glaring at the man.

"That is to be expected, but how strong _are_ they?"

"I can't be for certain. They're still learning how to control their attacks," he half lied, hoping it won't be seen through, or worse, they had been spied on.

"What _can_ they use?"

Casting his gaze down, he begrudgingly told the man, not having to see the near gleeful look in those eyes.

These were powerful attacks and possessed by beings cloned from a legendary Pokémon, which in turn would be powerful too.

"Excellent work, Professor Sebastian. You've done a marvelous job preparing them," Giovanni congratulated, making the other's stomach twist. "If what they learned is true, then I want to see it for myself."

"I'm afraid you missed today's battle, they're both exhausted and need rest," Sebastian spat, his parental instinct kicking in.

"I don't need some pathetic battle between them and some Bellsprout or Caterpie. No, I want you to bring them to Kanto instead by tomorrow afternoon. I'd like to see _exactly_ what they're capable of against a _real_ challenge."

Overhearing this, Cassie couldn't help but open her mouth, anger visible on her pretty face as she stormed over.

"You can't battle them with fully trained Pokémon. You'll end up destroying them! Even _we_ have to hold back with ours until they got stronger."

The scientist wanted to stop her, seeing others appearing, hearing her shouting, several grunts by their side.

"How do _you_ know they're not ready?"

"We've been raising them since they were nothing but cells. We know their limitations better than some selfish pig like you ever would! You see them as tools, but they aren't! They're alive and have feelings and _that_ has to be taken into consideration above everything else."

The insult got the man's attention, narrowing his eyes dangerously, watching as Davin came up, shoving her behind him protectively.

Without saying a word, he gestured for his bodyguards and secretary to follow him, leaving the lab.

Sebastian didn't like how the whole thing ended, having a horrid feeling in the pit of his stomach.

Dinner was silent, everyone unsure, knowing things were going to be rough, that their head scientist was going to have to return, whether he wants to or not.

Some have tried to convince him to simply run away, but he shook his head, telling them that it won't be like last time when Mewtwo escaped.

 _He_ knew what he was doing, the twins don't. They aren't developed enough to wipe memories as he had, however he had done it.

Even if he _did_ try running away, they would only put themselves and others in serious danger. They would easily be found and captured, the professor killed, possibly the twins too if they retaliated.

Then of course, there was the fact that Giovanni still has his daughters, could make a simple phone call and have _them_ killed.

Sebastian didn't think he could live with that kind of guilt, he carries enough already, has had enough people ripped from his life. He didn't want any more taken from him, not if he can somehow prevent it.

Climbing into bed, the professor felt hot tears forming, his body shaking, not for himself, nor his daughters, but for the clones.

Their days of play, their days of innocence is going to be over and there was nothing he could do. It felt like the day he failed to protect Amber's cloned body from being destroyed, the helplessness he felt watching Beta suffering in agony.

So wrapped up in his own thoughts, he barely took notice of the clones curling up in bed with him. Their innocent mewling was enough to draw him back, only to wrap his arms around them, hugging them close, tears finally falling.

How many times has he cried now?

How many times is he going to continue to cry?

When can he cry out of joy than sorrow?

When morning came, his belongings packed as were the two blank Mega Stones, knowing he would have to continue studying them.

He was planning to go to the train station, but knew if he did, he wouldn't arrive there until much later in the day.

He knew he was running late already, his body feeling sluggish with ever step he took, the clones clinging happily to his arms.

They were so innocent and peaceful, it broke his heart that he may inadvertently betray them, that they'll grow to hate him.

He didn't want to lose them, lose their love, he _had_ to think of something to keep their bond, keep _some_ fragment of their innocence.

When he arrived at the airport, the clones kept close to his side, he looked for his team, knowing they were due to arrive.

But none showed up, making his stomach twist once more, his anxiety growing worse until one face finally showed.

"Joel!" he called, seeing how miserable the man looked as he caught up. "What's wrong? Where are Davin and the others?"

"You haven't seen the news?"

"What?"

Making sure no one would listen, having his Kadabra out to keep the clones busy, he pulled the other away to talk.

"There was an explosion at the lab… Cassie, Davin, nearly everyone was there packing things up. It's been covered up as a gas leak."

"No…"

"I have no idea how much longer I'll live, you live…"

"He won't kill me, not as long as they need me, if there is a chance he wants more made if there are extra samples leftover or more are found. That _and_ he still has my daughters…" Sebastian whispered softly.

"Right…"

"And he won't kill you either."

"How are you certain?"

"Beta and Omega love you as much as they love me. They're going to be in enough shock already once they learn the others are gone. And you know a lot more about Mega Evolution than I do, and he's going to want that looked into still."

"Put it that way, guess I do have a chance," the man joked dryly. "But I honestly don't want to work for a man who'll throw away innocent lives as if they were nothing."

"Neither do I, not anymore, but I'm far to cowardly to try running away or to take my own life. Even if I did, what would happen to my daughters? To Beta and Omega? To you even?"

Giving him a pitiful look, he wrapped an arm around the other, the contact somehow easing the other, reminding him of Fuji.

"I'll stay then, seems _you_ need someone more than the girls do."

"I wish there was a way you _could_ leave, not be trapped here."

"I may be trapped, but Dialga _will_ forgive me in the end, and it'll forgive _you_ as well, I'm sure of it."

"Thank you."

Hearing their plane, the two gathered the Pokémon, climbing aboard, ensuring they kept together.

For the first time, Sebastian didn't hate being on a plane, drowning out all the noises around him.

He had at least one friend by his side, two energetic clones, seeing how excited they looked as they flew.

"Mew!"

Beta had let out an excited squeal as she ate a slice of apple that had been delivered to them by the stewardess.

She sat on Joel's lap; having a better handle keeping her from squirming all over the place and accidentally taking off down the aisles.

Omega was calmer, curled up in Sebastian's lap, staring out the window, obviously amazed at the height they were in.

She gently pawed at the glass, the professor gently scolding her that it's against the rules to open the window. Not that she could, but didn't want her to get ideas either way. Thankfully she listened, perfectly content to staring.

When they finally landed, gathering their bags, the clones staying close, both were surprised when a young girl ran up to them.

"Your Pokémon are really adorable," she laughed, kneeling down to their eye level. "Is it okay if I pet them?"

"Of course," the scientist spoke before he could stop himself, his sadness pushed back by how excited the clones were.

It was the first time someone came up to them, someone who looked so different height wise, age even.

"Mew!" Beta chirped happily, the two shaking hands, giggling away as was the girl, a bright smile on her face.

"Mew?" Omega chirped softly, taking notice of her bandana, obviously curious about it, the girl taking notice.

"Cute, isn't it?" she laughed as she let the clone touch it. "My dad sent it to me a little while ago. To bring me good luck while I'm in Johto."

"You're a Pokémon trainer?" Joel asked as he patted the clones as they nuzzled the girl, purring excitedly at the attention.

"I'm a coordinator actually. I'm going there to try the contests."

"I heard they just started opening them up, it should be a lot of fun," he laughed, seeing how much she beamed.

"I'm May by the way," she introduced, holding her hand out to the men, having them shake hands with her.

"I'm Dr. Joel Grittson."

"Professor Shiranui Sebastian."

"Oh wow, that's really cool. Are you visiting Professor Oak or something?"

"I'm afraid not, it's a different business we're heading to."

"And what are your Pokémon's names?"

"This is Beta and this is Omega, Beta's the older one," the professor spoke as he gestured to who was who.

"You know, I _swear_ I saw a Pokémon like them before," May spoke as she looked at the twins harder. "But it was a hologram; I didn't think it was real. You two must be really lucky to have them, getting to raise such cute Pokémon."

Both shared a worried glance, the girl missing it as she played with the two Pokémon some more.

Whether a blessing or not, they heard an announcement about the plane for Johto boarding, the girl almost jumping out of her skin.

"I'm sorry, I have to get going," she yelped as she gathered up her bags quickly.

"Yes, that's fine; you don't want to miss your flight," the professor spoke as he helped her get one of them over her shoulders.

"I hope to see you again, Professor Sebastian, Dr. Grittson!" she called as she started to hurry off before pausing once more. "Bye Beta, bye Omega, take care!"

Once she was out of sight, they made their way for the exit, taking various taxies and buses to get where they needed too.

When they arrived near the base, they were met by a van, various Rockets waiting for them.

Once there and inside, Sebastian felt his protective nature beginning to take over, he wrapped his arms around the twins.

He shot any dirty looks to anyone who knew what they were, the power they hold.

Joel stayed near, a demand the professor made, the two brought to an empty room with separate beds.

Looking around as things were set up, he turned to one of the lower ranked grunts, a scowl on his face.

"Where are Beta and Omega going to be?"

"In the basement with the rest of the boss' Pokémon," she answered flatly.

"I'm afraid that isn't acceptable. For their sake, they'll _both_ be staying with Dr. Grittson and I."

"Whatever."

Once they were left alone, Sebastian looked around, finding there wasn't a window, meaning he couldn't enjoy watching the outdoors. And knowing Giovanni, neither he nor Joel will be _allowed_ outside, not even the clones for a very long time.

Sitting on the bed, he buried his face into his hands, wondering what he ever did, how he never foresaw that he'd end up like this.

A hand patting his shoulder, he relaxed somewhat, knowing he at least has someone by his side.

He felt the clones climb into the bed, curling up, staring at him innocently, likely sensing his depression.

A bitter smile grew on his face as he looked at what he had left in his life, determined not to lose them.

* * *

 _ **Coming up with different attacks wasn't easy, especially the healing ones, wasn't sure about giving them** both **Heal Pulse, but figured it could act as a symbol to act as another example of the two being sisters. The other attacks were chosen again to suit and represent how they are.**_

 _ **Regarding May, I threw her in to give the idea of what the timeline is likely at, your choice to decide if this is when she** first **goes to Johto or her return trip after the Wallace Cup.**_

 _ **As for Joel, originally he wasn't, but ever since Gen 6 came out and Mega Evolution appeared... Yeah, gave Joel that role as a study, and he somehow avoids getting killed the first time round.**_

 _ **Please read and review**_


	13. Chapter 13

The next few months were grueling, the clones made to fight various Pokémon, Giovanni seemingly taking Cassie's last words to heart.

He made them fight strong, but much weaker Pokémon than his normal collection, a strange relief going through the two men.

The Rocket leader even allowed the clones to remain in the same room as them, than forcing them into cages.

It was quite obvious how close they were with their creator and with the younger scientist. Trying to forcefully separate them, especially now, would only lead to devastating results.

It only increased when seeing exactly _how_ powerful they are, Sebastian acting as their trainer, guiding them in battle. There have been a few times though Joel would take his place if to busy, showing the level of bond the two Pokémon held with both men.

Beta's Aura Sphere was destructive, if the Pokémon weren't as powerful as they had been trained, they would've been killed.

Omega's Future Sight, while taking a while to fully activate, it leaves scorches in the ground as if a bolt of lightning actually struck. Very few Pokémon are capable of that, not even Giovanni's strongest psychic types are capable of such destruction.

And this is while they're still young, not fully matured…

The Rocket leader could only imagine how much stronger they'll be when they _are_ fully developed, their powers fully matured.

But until then, they are useless for any real battles. They wouldn't understand, and even if they did, both would resist.

If he had been able to keep the gym, he could've used them to battle against various trainers for experience.

If only those bumbling three hadn't destroyed it, revealing it had been under Rocket hands, he would've been able to do more.

He would have to think of another plan to ensure they continued getting proper training, making them into perfect weapons for his goals…

Sebastian walked down the halls, reading some notes he and Joel had taken, to see if there is anything to find regarding the blank stones.

The younger scientist was retrieving the twins, their training session almost over, knowing they'll be tired and hungry.

Arriving in the cafeteria, he collected various things from the buffet, far more than he would normally take, but not all of it was for him.

Careful not to drop the notebooks _or_ the trays, he sat down at a table, ironically noting it was the same one he used to sit with Fuji.

Just as the memories of his time spent with the late doctor formed, as hot tears began to sting his eyes, it stopped when he saw familiar faces. More so as two ran to him, nearly knocking him over, mewling happily, their exhaustion ignored by their sheer joy over seeing their creator.

Both were sad by lack of play, having to fight so much, the battles no longer fun, yet they still found a reason to smile.

They clearly loved the professor, harboring no ill feelings towards him, not even towards Joel by how they would affectionately nuzzle and paw at him.

There weren't as many Rockets present in the cafeteria, many had gone to Unova following several rumors that could lead to their favor.

One was regarding some odd meteorite or something, but it had proven to be a bust, the thing having energy, but unable to harness it.

It had been sent back to Kanto for further studies, though its previous tests had nearly demolished it as did the travel here.

Other rumors related to some artifacts that could lead to controlling certain legendary Pokémon. As for whether it's true, Sebastian didn't care. He partially hoped that if it _was_ true, it is so heavily protected that Giovanni and his men end up getting killed trying to get it.

The latest rumor was regarding Team Rocket's greatest enemy, Caitlin Panthera, hearing she was _supposedly_ spotted somewhere in Unova.

The professor knew how much Giovanni hated that woman, wanting her dead, but it seemed far more than it should be.

Sure, she's ruined a lot of his plans, but so have others and he's practically letting them off scot free.

What makes her so different compared to the rest?

Why is he so hell bent to see her dead? To watch her fall?

Is it because she's captured legendary Pokémon?

That she raises Pokémon that _should_ be weak, probably put down, having them stronger than his own _healthy_ collection?

He couldn't help but admire her strength, willing to put herself in danger for others sake, protecting what she felt was right.

He hardly has that kind of courage…

If he did, he probably would've done something sooner, _far_ sooner to get out of this mess. He would've been willing to spend a few years to life behind bars if it meant getting Giovanni to join him, possibly sent to the chair.

His thoughts were broken when hearing a snort, turning to see Namba staring at his clones, making him scowl.

"What do you want?" he spat, the other now looking at him.

"I've been hearing _so_ much about your work since they arrived, I wanted to have a look," the balding man stated. "But seeing them now, they're pretty damn pathetic. I'm surprised Giovanni's even bothering with them."

"You wouldn't be saying that if you saw them in battle."

"Is that a challenge?"

"No, they fought enough today, they're exhausted. Any more and they could get seriously hurt," the professor stated, petting the clones.

"I don't know what happened, but ever since Project R's failure, you've gotten soft," the other spoke harshly as he walked off.

"Asshole," Joel sneered, biting into his sandwich.

"He's right though, I _have_ gotten soft. But it was sooner than that, he just doesn't remember," Sebastian sighed as he began to eat as well.

 **"R-remember?"** a soft voice echoed in their heads, both looking about.

"You hear that?" the younger man asked, seeing the alarmed look on the other.

"A child's voice?"

"Yeah… Wait, was it one of you?"

Joel looked between the Pokémon, seeing Omega staring intently at them, Beta far too busy trying to chew through a piece of tougher fruit.

 **"Remember? Remember what?"** the voice echoed, the Pokémon looking between them, showing it _was_ her who spoke.

"Someone we knew a long time ago," Sebastian sighed, giving a small smile of how far these two are coming along.

Already he's seeing they're getting bigger and bigger, their muscles developing, their skills sharpening. And now, they're beginning to communicate with telepathy, showing _just_ how far they've come.

 **"Who was it?"**

"A special man, he was the one who found you two, your DNA to be precise."

 **"Is he like a papa?"**

Eyes widening, feeling tears beginning to form at the edge of his eyes, he blinked them away, giving a sad smile.

"Yes, that's exactly right. You could say he _was_ your father. He may not have directly made you, but if he hadn't found you, had the knowledge to make you as you are now, neither of you would be here."

 **"Where is he?"**

"He passed away a long time ago."

 **"He made you happy, didn't he?"**

Before he could stop them a second time, a couple of tears fell, nodding slowly than voicing it, feeling her brush his face with her paw.

Despite her age, she was so much more mature, far more aware of her surroundings, but she was still so very kind.

 **"Why didn't he make us?"** a different voice asked, the two figuring it was Beta.

It was confirmed by how she looked up, having finally won her personal fight against the fruit, the juice all over her muzzle.

"He was making another, a very special one, a big brother," Sebastian answered as he used a napkin to clean her face.

 **"A big brother? There are more of us?"**

"Yes, but he's on a very _special_ vacation and won't be back for a very long time."

 **"But if we have papa, does that mean you're our mama?"**

The question made the professor nearly choke on his coffee, Joel unable to suppress a chuckle by how red his face became.

"I don't know if he's really _mother_ material, but he's got the right instincts," the younger man teased, ignoring the scowl sent his way. "He loves you two very much, you know it and he knows it."

"Of course I love them, they're like…"

"Like daughters?"

"I…I guess…they are, they really are."

Turning back to the twins, watching as they continued to eat, it made him wonder if he really _was_ more like a mother.

When his daughters were born, he was so happy and cried so much when they were taken away, where he couldn't see them, know how they're doing.

He was willing to do anything and everything for them, not to buy their love, but show them how much he loved them, was willing to protect them.

While he never got to raise his daughters, it was almost like given a second chance, raising the clones.

They weren't human, yes, but they were still alive, bore very human emotions, are very much children.

They looked up to him, relied on him for food, a warm place to sleep, hug them when scared. But most of all, he _had_ given them plenty of love and affection that they both deserve and need, and continues doing so.

It didn't help that in his past fantasies of Fuji, he not once thought of himself taking control, letting himself be controlled instead. Even before meeting him, when he had been married, he wasn't as dominating as he probably should've been.

He was not a leader, didn't matter if he was left in charge, it didn't mean that he was an _actual_ leader.

He's used to taking orders, looking to others stronger and smarter for guidance and in some ways, for protection.

A gentle nudge grabbed his attention, turning to see Omega nuzzling him gently, a smile on her face.

 **"I don't care if you're a papa _or_ a mama. You've been raising us, you and Joel together. You're _our_ family. If our other papa was around, we'd love him too, but we would always love you most."**

"Thank you, Omega," he smiled, "you don't know how much that means. You don't know how lucky I feel having been picked to watch you two grow up."

"After watching you two grow from a clump of cells into two loving and kindhearted Pokémon… It really _has_ been a blessing," Joel added, leaning on his elbows, a warm smile on his face.

Feeling much better, Sebastian drank his coffee, taking bites of his lunch until all of them had their fill.

He continued to dote on them, ignoring stares and comments made by others, encouraging them as they continued battling, tend to them when injured.

Slowly word came back that Giovanni and his men were returning, hearing from those who returned sooner about their failures.

Not only was Panthera _not_ in Unova as they had hoped, but whatever artifact they searched for nearly drove the leader insane. He was in rough shape, having been bedridden for several days, the professor catching a glimpse.

When they first returned, even if it took a day or two to by plane, the man was in awful shape he almost pitied him. The leader was pale, nearly carried to his private chambers, mumbling something that could be a dream or disoriented orders.

Whatever had happened, it must've drained him tremendously, and knowing the stubborn bastard, likely held up a façade that he's okay. Either way, his pride is wounded and will need time to recover until then.

And it was very much like that, once he recovered, giving orders out to various Rockets, there was a strange change.

Certain orders seemed normal, namely to specific teams he uses, specifically one group that has been traveling about the world.

Yet there have been times where he became much crueler, reviving some old plans that failed, usually due to the three aforementioned.

And with Panthera in some far off region, she wasn't here to stop him as he began to gracefully take over.

What more, Giovanni, his identity as the leader of Team Rocket still unknown _finally_ reclaimed his position as gym leader.

He fabricated a lie about having been held hostage, even having his more talented agents fabricate the right kind of evidence to make it appear so.

It was a rather excellent plan, when it made the news, the professor catching a glimpse as other Rockets watched.

Seeing him with a fake smile, looking somewhat sickly as if starved for some time, it was rather pitiful and sickening.

Sebastian couldn't believe how _gullible_ people were, yet couldn't help but pity them too, seeing just how much of an actor Giovanni really was. If he hadn't known the man as well as he does, he would've fallen for it too.

How he managed to pull it off, he wasn't sure nor was he interested, partially listening to the leader speak with absolute joy of being found.

Hearing him talk how grateful he was for such loyal friends not once stopping to find him, the professor couldn't help but feel sick.

Once he returned, the façade he put on for the news, for fellow gym leaders was gone, replaced with the same look as always. It was as if he were two different people trapped in one body, one who wanted to do good, the other wanting to do harm.

Sebastian almost jumped when called to the leader's office one day, leaving the clones with Joel to watch.

Arriving at the office much sooner than he would've liked, he stopped when hearing him talking to someone inside.

Unable to resist, he stood just close enough to listen, the door cracked enough to make out what was being said.

"You don't realize how much in debt I am to you for getting my gym leader position back," Giovanni's voice spoke, clearly thankful to whoever was with him.

"It was nothing, a human's mind, even these psychic Pokémon are rather pitiful and easy to trick," a woman's voice, clearly not his secretary's, chuckled. "The only ones that were a tad more challenging were the girl from Cerulean and the boy from Pewter, somehow knowing your identity."

"Yes, I'll have to find out how _that_ happened…"

"Tread carefully, Giovanni. You're lucky Panthera doesn't know your identity."

"I know," he growled softly at the name before calming down. "Give my regards to your sister, and anything she wants, Team Rocket will give full support."

"Of course, you'll get to rule this world and she gets to rule everything else. And I'm sure if you make her _exceptionally_ happy, you may find yourself ruling more than one world."

 _"What the hell?"_ Sebastian wondered, feeling his heart racing, unsure if what he heard was correct. _"Is this woman some sort of demon?"_

He knew demons lived in their world, but they were extremely rare, almost reclusive, hardly ever seen. There's only a small handful that are known or rumored to be demons, the most notable being a trainer who's strength is on par with…

"Oh, and your orders are to not only find Panthera and her children, but kill them as well. I _hope_ you haven't forgotten."

"You have nothing to worry about. Panthera's been a thorn in my side for quite some time. As for killing her children, they'll just be the icing on the cake. It'll simply be _finding_ them, Panthera especially, that is troubling."

"It is of no surprise, being who and _what_ she is, she _would_ be difficult to trace regardless of her popularity status. But I'll give you a hint, if you manage to find _one_ of her kittens and make it known; I _know_ she'll come running. Family is _everything_ to her; she would trade her very existence to keep them safe."

"I'll keep it in mind, thank you, Eclipse was it?"

"That's good to hear."

Hearing footsteps, Sebastian squeezed his eyes shut, believing she was walking out, find out he was listening in and kill him.

She _had_ to be a demon, she had to and the very knowledge terrified him.

Not hearing the door open fully, he slowly cracked an eye open, seeing the empty hall, wondering if they were discussing some more.

"Professor Sebastian, I know you're there," the Rocket boss' voice spoke, making the other nearly leap out of his skin.

Swallowing hard, he just barely composed himself, walking into the strangely chilling office. It wasn't necessarily cold, but it felt it, as if someone was there, sizing him up, someone who _isn't_ the man sitting before him.

"How has your research on the Mega Evolution gone?"

"Stupendously, a lot has been discovered and I've made several theories regarding it. However, until Hun returns with a Key Stone, I won't be able to test those theories out properly. A simulator and equations can only do so much before an actual field test becomes necessary."

"Of course, of course," he smiled, making the other break out in a sweat.

Why was he so scared?

The demon was obviously not here, having taken some other route to leave, avoid being seen.

Or was she _really_ gone?

She could be hiding, the office is large and there are other doors, visible and hidden, a window disguised as a mirror even. He knows, there have been a few times he's stood behind it to study if a particular meeting is held.

"Those stones you collected? Have you found out anything about them?"

"Not much I'm afraid. They carry an unstable energy and there is no current piece of technology that could be of help. The closest would be having one or both make contact with a Pokémon while in battle and record the patterns as they change into Mega Stones. Even then, I can't be certain, despite how many years it's been present, study wise it is still very new."

"Why are you so nervous, Shiranui?"

He felt his breath hitch, having never heard the man call him by his name, only his surname and title.

"I don't know what you're talking about."

"You seem rather anxious, are you worried about my previous meeting?"

" _Other_ meeting?"

"Don't play dumb, it's clear that you heard."

"Just the part of you having to take out Panthera, but that isn't new. You hate her for ruining many of your plans as often as those kids three of your men chase after."

"Ah, yes, Caitlin Panthera, did you know she's not even human?"

"I wasn't aware…" Sebastian answered softly.

Of course, he's held some suspicion, having seen her photos and televised events relating to her.

From the years she began to current dates, she's barely aged if at all. So her not being human makes sense, though _what_ she is, he couldn't be certain…

"No, she's actually a creature from the stars, another world, dimension to be precise. Yet she's here, meddling in _our_ world."

"She is? I know there are rumors of life beyond our world, mainly through research done on Deoxys…"

"Yes, but she's _far_ more special than Deoxys."

"Is there something you want me to do regarding her?"

"Yes, I'll be sending some of my best agents to try and find information about her, including who her family may be or people she is closest with."

"But if her children are young though, why kill them? They could simply be taken and made into more operatives…"

"Rather cute how you seem to worry about children even though yours have already aged into adults. You try to hide it, but it's obvious you _do_ care about their safety. It explains why you never once sent orders to kill those brats who freed Raikou and destroyed the Miracle Crystal. Nor did you make _any_ attempt to kill the brats who participated in the destruction of Project R."

He didn't like how Giovanni was acting, how sickly sweet he was, it was obvious he was toying with him.

The look on his face was evident, even the way he spoke…

What sort of game is he playing?

"You _really_ miss your daughters, don't you?"

"Of course I do. If I didn't, you wouldn't be using them to keep me here."

"That's _right,_ such a good father you are. Even if you never saw them once, you never stopped thinking about them. You staying here, it was all for them, to _someday_ meet them, reconcile with them, wasn't it?"

"Yes…"

Was he going to let him see his girls, or did he do something to him?

"It's that kind of love that may very well help locate Panthera."

"What?"

"You two have similar personalities, willing to do just about _anything_ to see your family safe from harm."

"So you want me to find her and befriend her? But being that she isn't human, she would likely see through such a ploy."

"Not befriend, but try to _think_ like her."

"I don't understand, why me?"

"As I said, you two are similar when it comes to family. If you can think of how she may act, learn more about her, it may make tracking her easier. And if not that, find out who her children are. If we can get even one, we can use them to draw her out in an appropriate trap and kill them both or all if we're lucky enough."

He about to argue, to refuse such a cruel job, but the glare sent his way made him silent, knowing that if he rebelled, his daughters would suffer. And not just them, but the clones, Joel even would suffer.

 _"He's using my love for my daughters to kill someone, to kill a mother,"_ the other mentally shuddered, squeezing his eyes shut.

"I expect some sort of report by the end of the month."

* * *

 _ **Professor Sebastian now has to use those same parental instincts to help locate an enemy of Team Rocket, either by locating one of her children to use as a hostage or find her, herself.**_

 _ **Think it'll be easy for him, or simply make things much harder for himself emotionally?**_

 **Note:**

 _ **Those who don't know Panthera, she is an OC who has appeared in other pieces and is the same, having a skill to travel dimensions. More info will show up down the road, a possible bio being made later up on Deviantart under the same name as here.**_

 _ **Please read and review**_


	14. Chapter 14

There was so little known about her personal life to give him any leads of where she may be, who she might be related to.

The only thing that _could_ be found was through the media scattered about the internet, most already collected than hunting it himself.

He read and listen various interviews or battles she entered at any of the Pokémon Leagues or other known competitions that'd draw someone like her in.

It was like this for a couple of days before dozens upon _dozens_ of files, hard and digital copies alike were dropped off.

Going through them, Sebastian was in awe, learning far more about her, amazed at what she's capable of, finding out just _how_ intelligent she really is.

There was so little known about her personal life, what is known in the media, recorded interviews and battles is all he had to go by.

At least it was like that until dozens upon dozens of files, hard copies and digital alike were dropped in the room.

He probably _could've_ asked for a different room to work in, but being he, the clones, and Joel were rarely apart, it was easier to just dump everything here. Anything that couldn't fit were put into a nearby closet. From there, he would go to fetch the binders or put one back when done.

Not only was she a brilliant tactician when it came to battling, but for actual military use.

It explained how she could win so easily…

She's been using that experience for battling, toning it down to avoid seriously hurting other Pokémon and possibly trainers. She even trains certain ones to use specifically for protecting civilians in case a battle got out of hand.

She's one of few trainers allowed to have more than six _for_ that sole purpose, more so upon becoming champion and gaining ranks amongst police and rangers.

And yet, despite her holding back during competitions, he's heard how vicious, brutal she can be fighting illegal operations. Whether it's against Team Rocket, hired hands, anything, she's almost always there, leaping from the shadows to tear them down.

And it isn't her Pokémon that leave piles of bodies behind…

At first, he didn't think something like that was possible, not even demons having that kind of strength to hold their own against a Pokémon. But after reading through the tenth binder, he now understands.

She uses magic, _powerful_ magic, something he wasn't about to toss as nonsense, not after what he's been dealing with lately.

She's extremely brilliant, not surprising due to what sort of Pokémon she raises, having seen the prosthetics she's designed for her Pokémon. Even others she's designed for those that are to stay wild, but kept in a nature reserve for its sake. Not only that, even if he didn't believe in magic, it takes great knowledge to learn it.

In the end, it was impossible to think she was human, not even any demon he's heard of in history and media.

He soon found himself becoming as immersed in her life, admiring her strength, her courage, her intellect, her kindness most of all.

If things had been different and met _her_ instead of Giovanni, he likely would've been much happier. Especially if she trusted him enough to share her secrets than what most she may consider friends here may know.

But it wasn't just her alone, what she can do or has done that made him amazed, but her family too.

Many of the names were strange, not recognizing that many when comparing them to the names from his own world. Some of the names were even disorganized, mistranslated, having to wait until it was fixed.

He was informed that the language used was very old, roughly the very first to come into existence, surprising him of just how old the species was.

The closest he got was information on the woman's younger brother, a talented coordinator oddly enough. But he's much like his sister by means of being an enigma, more so as he's almost _always_ traveling with her. Therefore, using him as bait was out of the question. Even if they _could_ get him, he's just as dangerous as her, so may end up backfiring trying to kidnap him.

Despite that, the very thought, of her not only from another world, but another _dimension_ , it was almost surreal.

No, not surreal, it was absolutely terrifying…

The normal voice in his head, the voice that would urge him to get excited over discovering something new, it was silent.

He wasn't sure whether to be grateful or become even _more_ afraid, to take it as some ominous message.

Sitting back, he let out a groan, removing his glasses to rub his face, exhaustion clawing at him. Because Giovanni wants monthly reports about Panthera, about _anything_ and there being so much, he's gotten so little sleep.

But it wasn't just the short deadline that kept him awake. He's been hearing rumors spreading about headquarters, strange and terrifying rumors.

Various grunts, mostly newbies and those considered useless, vanishing, never being seen again. It didn't help that at the same time they began disappearing, an increase of homeless and various species of Pokémon also began vanishing.

It was _that_ , that caused the Pokémon Leagues to start reinitiating the old laws. It was to try and help species of Pokémon repopulate from the sudden increase of poaching.

He felt Giovanni had a hand in this, but wasn't sure nor _wanted_ to call him out on it. He didn't want to risk begin next, or risk anyone close to him being next.

Each month that passed, the clones grew bigger, silently thanking Dialga for letting him continue seeing his creations.

They were much older, maturing more, their baby faces slowly changing to a more adult look, though their heights were still short.

They were big enough where neither he or Joel could carry even _one_ of them if they wanted to. They were simply too big and heavy for it, having to explain it to them, mostly Beta due to her excitement, knowing she's usually the first to _"attack"_ them.

But to make up for it, the girls _now_ take turns picking him and Joel up if either were too tired to go down a hall or return to their bed. Yet it showed how much stronger they've become, how caring they still are.

Despite being a psychic type, Beta has impressive strength, perfect with her physical prowess and usage for a full assault of attacks.

Her sister on the other hand, Omega, wasn't as strong physically, therefore would rely more on her psychic control.

Soon enough, couple of years had passed, feeling more tired and lost, wishing he could simply disappear off the face of the planet.

Letting his head hit the desk, unable to keep his eyes open much longer, he was nearly asleep before something was draped over him.

Cracking an eye open, he saw that it had been Omega putting the blanket over him, unable to suppress a smile.

She knew she couldn't put him to bed; he would have to wake up at least within five, maybe ten minutes and resume work. He just needed to rest his poor eyes, wondering if all these late nights and long days would end up ruining his sight any more than it already was.

Letting his eyes shut, he was soon in a peaceful sleep, body relaxing as he used his arms as pillows.

Omega busied herself in setting the alarm to wake him at an appropriate time so he wouldn't be too drowsy nor end up grumpy.

She wished her creator, her father, wouldn't work so hard as she removed his glasses, seeing he forgot before dozing off.

But he had told her that he had to, not because he wanted to, but because he _has_ to for the sake of himself and his loved ones.

She didn't want to think what would happen if he's unable to complete whatever Giovanni ordered him to do.

When he woke up, the alarm buzzing close enough to grab, he blinked a bit, almost forgetting what he was doing.

When glasses were back on and the unfinished reports were legible, he frowned as he recalled it all.

Compiling what he could, he barely finished before the end of another month, handing the folder in and leaving as quickly as he could to get some decent sleep.

Back in his room, he collapsed onto the bed, curling up, feeling so lightheaded, unsure if it was due to fatigue, illness, or maybe guilt. Though with his luck, it probably would be all three, guilt taking the most room.

"Hey, you should eat something," Joel's voice spoke up, grabbing the weary man's attention when smelling food and coffee.

"No coffee, I want to sleep," Sebastian grumbled, trying to burrow deeper into the blankets before they were pulled off, making him groan.

"No worries, _this_ is for me, but _you_ are going to at least take a few bites. You gave the girls and I a real scare the last time."

Realizing he was in a losing battle, the older man gave a groan as he forced himself up into a sitting position, deciding not to use his glasses. He can eat without them on, his vision's poor, but not _that_ poor.

"I don't even recall how it happened."

"Not surprising," Joel answered as he handed a sandwich to him.

"I've never been this exhausted before. Not even final exams in college were _this_ bad," the professor half joked after taking a few bites.

"I know what you mean," the other muttered after swallowing. "I've also got a bag of chips and some soda."

"No caffeine," the professor half whined.

"It's non-caffeinated," the younger man laughed at the other's actions, knowing he wouldn't do this in public willingly.

"Where are they?" he asked, not needing to specify any more than that.

"Training… Shiranui, if I may ask… What exactly _has_ Panthera done to Team Rocket to garner such attention?"

"It isn't just Team Rocket. She's pissed off _a lot_ of people, those who are part of underground trades, black market, tyrants even. In short, truly evil beings hell bent on making _all_ our lives miserable."

"What are the chances she'd win in the end?" he asked, clearly having read some of the reports or notes, but not enough to know the entire thing.

"From what I read about her…not very good," the professor sighed sadly, staring into his soda.

"Seriously?"

"It isn't because she's weak or childish. She's brilliant, powerful, she has this talent to influence others to work with her. But at the same time, many she has join her often have squabbles amongst themselves, most of it race related. And if not race, it could be discriminations with gender, religion, any of those things or combination."

"I see, even _with_ a powerful army on her side. If they can't get along, it would be like fighting alone."

"Exactly, and from what I can presume, whoever, _whatever_ Darkness is, she would take advantage of it and crush them all."

"You'd think the whole cliché stories of good guys always winning would have an impact here too."

"Panthera _could_ still win; she does seem to have this other gift pulling miracles out of nowhere. But those are just individual fights. If she were to get into an _actual_ war, allied forces joining her, _that's_ where it could get shaky. A majority I'm sure would put differences aside and work as one to defend themselves."

"But the few that don't could end up causing a serious backlash."

"Yeah…"

"You think _we'll_ ever get out of this?"

"No… Not alive at least…"

"True…"

"Joel, I'm _so_ sorry you got dragged into this."

" _You_ didn't drag me into anything. _I_ said yes when Thomas offered to hire me. _I_ chose to stay by your side to help continue the research and care for the girls. Everything that's happened, they've all been _my_ decisions."

"Then why did you decide to stay? Not make an attempt to flee? You could have with your Kadabra. A simple teleport and you would be gone, continue teleporting around until you got to a ship or even a police station, Pokémon League even. You could've left the country, gone to the Sevii Islands, the Orange Islands, an isolated part of Johto like Mt. Silver to lay low."

"I had a reason to stay…"

"What reason…"

His question was interrupted when a pair of lips was over his, a hand gently cupping his cheek, thumb gracing the side of his face.

He felt his eyes widen, not realizing he gasped, unintentionally inviting the other to explore his mouth. The younger man's tongue explored him, tasting him, the other unable to suppress a moan.

He could pick up the taste of the other's lunch, tasting the various vegetables he just ate, and oddly enough, a sweeter taste. It was almost like cinnamon, briefly wondering if he had something like that earlier.

A part of him wanted to fight, to resist being kissed so suddenly, not out of fear, but confusion, wanting to know why.

And yet, he didn't want the kiss to stop, wanting it to last forever.

It felt so nice, felt so comfortable, the way a kiss should always feel…

However, the need to breathe forced them to part, both staring at one another.

The younger man rested his forehead against the other, a look of guilt shining in his honey eyes.

"I'm sorry, I shouldn't have done…"

"Don't apologize, I liked it…I liked it a lot," Sebastian admitted, feeling his face heat up. Being this close, he could see the other man's cheeks turn a darker shade. "But I want to know though. When did you…did you start liking me?"

"When you tried to clone Amber. The way you lit up, the idea of raising her, fulfilling that promise… I found it stunning. And it just grew as we worked on the girls. Corny as this may sound, but you looked beautiful when you held them, shushing them as they cried, calming them down. I knew it then, I knew I was completely head over heels for you."

"I'm not _that_ good looking."

"You are, you just don't let yourself see how gorgeous you are," Joel spoke, reaching a gentle hand out, stroking the short hair, teasing the stripe.

"You don't want someone like me though."

"And why not?"

"You don't want to know…"

"Did someone hurt you?"

Sebastian turned his head away, his lack of sleep _really_ screwing with him and now having a friend confess like this.

If he wasn't so exhausted, he would've pushed him away, not wanting to risk getting any closer.

Part of him just wanted to go somewhere, curl up and hide from the world…

"If someone hurt you, that's not your fault."

"It isn't just the rape!" he snapped angrily, only to pale when he realized what he just admitted.

Thinking that Joel was going to say something hurtful, maybe even leave him, either in disgust or shame, he was shocked when arms wrapped around him.

" _That_ isn't your fault though," he comforted, petting the other's trembling back.

"It isn't the rape alone though," he repeated softly, burying his face into the other's shoulder. "You know that I was married before, right?"

"I know, but not to be entirely rude, but she's a complete bitch."

"I didn't know, or refused to accept it at the time when we were together. I was just a stupid kid back then. But like any stupid kid, I was easy to trick. I was such an idiot back then…"

"Shiranui," Joel spoke, looking the other straight in the eye, the other making his features out. "Times I've seen her, have had to _interact_ with that woman; she's a sadist."

"I know that now, but back then…"

"She took _advantage_ of you, in ways no one should _ever_ do to another. But that _still_ isn't your fault."

Gently, he cupped the man's face, a pleading look on his face, the other looking so unsure, scared even.

It was a rare sight to behold, something he wished he _didn't_ see, but at the same time, he was glad. It meant he trusted him enough to show his real feelings, meaning he can heal so long as he had the right people in his life.

"Sounds like something Thomas would say," the other laughed half heartily.

"I guess it does, doesn't it?" he chuckled softly, unable to help but lean his head into the other.

What he didn't expect was to feel the older man's hands grab the front of his shirt, pulling him closer to his body.

Nervous lips connected with his, letting him deepen the kiss, hearing a soft moan, knowing he was enjoying himself.

Shifting slightly, Joel began to let his hands roam, careful not to move too fast.

Now learning he had been raped, he _couldn't_ move to fast, not wanting to accidentally make the other remember something from that day.

No, he was more than content to stick with what they're doing, to go as slow or as fast as the other wished.

The brunette couldn't help but slowly push the other onto his back, climbing on top, one leg tucked between his superior's.

He let his hands explore, pushing the shirt upwards to expose his stomach and chest, the other taking sharp breaths.

"Joel…" he moaned when a hand rubbed his side, fingers dancing across his ribcage so gently.

Neither knew how long it had been, both men simply touching one another, discovering what made the other gasp or moan, whimper and growl with need.

Another gasp escaped the older scientist, arching his back when a particularly sensitive spot was touched, his hips grinding into the others.

Joel smirked as he planted one kiss after enough down the man's jawline and neck, careful not to leave visible marks.

Finding a spot at the joint his neck and shoulder connect, he began to lightly suck on it, gently nipping, hearing the other cry out.

Sebastian was shivering with pleasure, having not felt this good in years, turning his head to one side, exposing more of his neck.

He didn't think the man's stubble would feel this good against his skin, grateful he rarely shaved if it meant feeling like this.

Rubbing his hands across the younger man's back, hearing him let out a deep growl, a sharper bite made, enough to make him gasp. However, he continued, wanting more, to make the other react as much as he had made him.

The scientist felt his whole body heating up, whimpering by how tight his slacks were becoming, feeling the other's arousal pressing into his thigh.

However it ended the moment a hand began to play with his belt, the other hand attempting to descend down, his mind went blank.

Second Joel heard his breathing hitch, no longer trembling with desire, he inwardly cursed as he pulled away.

He cursed himself some more seeing how scared the man looked, tears just starting to form, his flushed skin paling.

The brunette sat as far from the other, giving him as much breathing room as possible, not wanting to frighten him further by holding him.

"J-Joel, I'm sorry," Sebastian finally spoke, his voice soft.

He was trying to control his breathing, trying to remind himself that this was _Joel_ , not his rapist.

"Don't, I got carried away, I should have moved slower," the other spoke, taking the risk to move closer, wrapping his arms around him when he sat up. "I'm sorry, you went through something traumatic and I nearly made you _relieve_ it."

"I thought I was over it…" the other whispered, resting his head against the other's shoulder, clinging to him for all it was worth. "I stopped having nightmares and what we were doing; it felt so good I didn't _want_ to stop. I don't know why I panicked."

"I'm not a psychologist, but something like this; it can't easily be gotten over. It takes time to heal."

"I know that, but I honestly thought…"

"It's okay, we'll take our time, go as slow and as fast as you wish," Joel reassured, planting a gentle kiss on the other's forehead. "Why don't you get some rest? You really need it and I think I kept you awake long enough."

"Stay with me?"

A little confused by the request, Joel looked at him as he put what wasn't eaten away, the rest going into the trash.

When he turned to look back at the other, he noticed that he had moved over, giving enough space to crawl into bed with him.

"Are you sure?" he asked, not wanting to cause him another panic attack.

"It isn't like we're having sex," the other stated, a small smirk forming.

"Fair enough," he laughed as he walked over, kicking his shoes off.

As he removed most of his clothes, keeping only a tank top and boxers on, he spied the other doing the same until he was nothing but boxers.

Climbing in, the brunette wrapped an arm around the other, feeling him settle comfortably, his breathing slowly steading.

Smiling softly, he planted one last kiss on his lover's lips before letting himself fall fast asleep.

"Night, Shi."

* * *

 _ **Seems the professor's finally found someone to love him for who he is, if you ignore the little hiccup they had that is.**_

 _ **Would you believe that I'm really enjoying Joel myself? He went from a minor character who was going to die much earlier in the chapters into this?**_

 _ **I just hope that I didn't make the near end** to **fluffy or corny.**_

 _ **Please read and review**_


	15. Chapter 15

The rumors from before, the ones about people and Pokémon disappearing?

They've become _much_ worse now, now including rumors of possible experimentation being done, led by Dr. Zager and several other scientists.

Sebastian feared that if it _were_ indeed true, he would be swept away, made to participate in some manner, yet it never happened.

He later rationalized it with the possibility that due to the clones; they really _can't_ take off with him as freely as before.

If they did, he may snap as would they because of their bond.

And now that he's forming a relationship with Joel, he doesn't want to think about being separated from him.

He doesn't want to be sent to Arceus knows where on some secret lab, away from him, away from the clones, away from his family.

But it still didn't stop his paranoia growing, one day hearing about Attila and Hun going missing. Nothing left to trace them, almost as if they didn't exist if it wasn't for the fact people knew them, at least in name to know their status.

Then there's the fact that he knew them far too well, Hun especially. They wouldn't simply leave Team Rocket just like that, not with their positions. Not with the few friends they've made and promise to help out with the clones if needed.

In the back of his mind, Sebastian knew they likely were taken, either tricked or had been ordered to work in whatever project Zager and the others are doing.

Whether they were ordered to kidnap people and steal Pokémon or are part of the experimentation themselves, he dared not dwell on it.

The scientist shuddered, arms wrapping around himself, thinking about all those missing people, most of them as young as ten.

The latest kidnappee was a young boy, seeing his photo on the news, parents desperate to find him and his Pokémon.

He felt horrible for the families, knowing these missing people and Pokémon are likely here or some other secret base. He figured the latter or there would've been more activity and gossip going around.

The closest thing next to Joel and the clones to keep him somewhat sane was his research on Panthera.

If he didn't figure out how to find her, who knows what Giovanni may do to them if he deems his research to slow or lacking.

He knew in the back of his mind, he should be cursing himself for getting so close, not so much with Joel, but the clones. They're Pokémon, yet they're so much more than that. He was feeling more and more like a father as the days go on, always teaching them something new.

It didn't help that they view him as their father, or _mother_ as Beta sometimes puts it, calling Joel the father.

Yes, the two somehow figured out they had gotten together, though it may not have been all that secretive to begin with.

When he's around the clones, Joel even, he simply felt little need to hide secrets less it was meant to keep them safe. Such as not telling the girls the complete truth of Team Rocket, knowing someday he may have to before it's too late.

He doesn't want to hurt them, not while they're still young, having yet to truly see how cruel life can be at times.

Both of them try so hard to do good in their training sessions so they can rejoin him and Joel as soon as possible.

They've gotten better using telepathy, the things they say sharper and clearer than distorted. It's almost like they're _really_ talking.

If it wasn't for the fact their mouths don't move when they _do_ speak and no one else hears them, he would have thought they somehow learned like that Meowth.

Of course, they choose _who_ to speak with, those they trust such as the two of them, even choosing to trust Tyson.

Both bonded with the man, Beta mostly by how she'd momentarily forget her strength and tackle him down, greeting him.

Sebastian can still remember the look on the man's face; it was rather priceless the first time he heard them speak.

Whether it was that, Beta knocking the wind out of him, or the fact they both started calling him their uncle, he wasn't sure. Tyson was rather embarrassed, yet happy at the same time, as if he found a reason to _be_ happy.

Lost in his thoughts, the scientist nearly walked past Giovanni's office, snapping his mind back into focus as he lightly knocked on the door.

Given confirmation to enter, he did so, handing in his latest report, standing there, eagerly waiting for dismissal as the man thumbed through his work.

"Very good, Professor, you're doing a _very_ good job. Now all we need to do is figure out if any of her _kittens_ are here in our world."

"I still don't understand why we should murder children. With the right tools and training, we could easily turn them to our side…"

"In case you've forgotten, they aren't _ordinary_ children, and not all _are_ children. Do not let her appearance fool you, Panthera is _far_ older. She has offspring who range between child and adult."

"And if those adult children of hers, what if they have families? Including their reincarnated ones?"

"If her adult children have had children of their own, then we shall treat them as if they're Panthera's own."

"Even if they're newborns?" Sebastian asked, horrified by what he was hearing, what the other was implying.

"It just makes the job easier."

"You…you sick bastard! I didn't sign up for this! Murdering someone like Panthera, high classed trainers, League trainers even are one thing, _they_ are a threat to you. But murdering defenseless children? Have you gone completely insane?" he screamed, unable to keep his composure, slamming his hands down hard on the desk.

"Don't act so innocent my dear professor. If you recall, you've participated in some rather _gruesome_ experiments that are on par to what _I'm_ willing to do. Remember all those Eevee I provided?"

"I remember, including every other sick experiment you gave me. I'm not innocent, I admit that much…"

"Then what's the problem now?"

"As if you'd understand," Sebastian spat, storming out of the office.

He knew it was a risk doing that, for blowing up like that and leaving without permission. But if he stayed a second longer, he _knew_ he'd end up doing something he would _really_ regret.

Storming into his room, he inadvertently startled Joel whom was at his desk, toying with the remains of the meteonite.

Ignoring everything but his own angry thoughts, he threw himself onto their bed, a muffled scream thrown into a pillow. The action was childish, but what other option did he really have?

"Shit!" the younger scientist cursed, dropping the rock, but chose to ignore it to see to his lover. "Hey, what happened?"

Calming down, he lifted his face from the pillow when feeling the bed dip slightly, a hand landing on his back, going in gentle circles.

"The usual," he answered with a soft growl.

"Tell me anyway. Might help."

"You _really_ don't want to know."

"Maybe, but I'm asking anyway."

"G-Giovanni is willing to kill not just Panthera, but her children, even _their_ children if they have any. He's even willing to kill any of their families they were reincarnated in if it makes things easier for him."

"What?"

"I tried to reason with him, to at least spare the really young kids…"

"But he wouldn't listen?"

"What do you think?" he spat, hating how he sounded, seeing how upset the other looked. "I know he hates her and this shouldn't be a surprise, but the extreme he's going, it's too much. It doesn't matter if he's under orders or his own; he's making _us_ do his dirty work in the end."

"There has to be a way to get out of here."

"I can get two spots open in the morgue."

"This isn't a joke, I'm serious!"

"So am I! This Darkness, she…she has influence all over the world, possibly beyond our world, our dimension. I've walked in on meetings between her and Giovanni, with other people from our world and the next. You wouldn't _believe_ how insane they looked, not just their eyes, but _physically_ insane."

A shudder ran through him, the other gingerly petting him, trying to settle him down, seeing how scared he was.

"There has to be a way though…"

"I wish there was, but with what we have here now, wandering our base, I don't know how we could even _think_ to escape."

"Shi…" Joel sighed, unsure how to bring him out of this.

"I'm scared; I never felt this scared since I was raped, since Giovanni threatened my daughters. I don't want to die here; I don't want you or _any_ of the girls to die here either. But I don't have a single clue."

Tears began to fall from his eyes, cursing his weakness, wishing he could be stronger, that the mask he used to wear was real.

If it was…

No, if it was, he would never have met Fuji, joined the project let _alone_ come to love his creations as if they were his own. Most of all, he wouldn't have ended up truly falling in love for the third time in his pathetic life.

"Shi, sit up, please," Joel's voice begged, the other doing so, unable to refuse, not wanting to refuse.

Just as he did, facing the other, glasses slightly askew from throwing himself into the bed, he let out a gasp when pulled into his arms.

"We'll figure out a way, we'll figure out how to get out of here, get the girls, your daughters out too."

"Joel…"

Pulling apart, he was surprised when the other reached behind his neck, tugging a silver chain to unclasp it, pulling it free.

He remembered seeing it before; it was a pendant his lover wore, a symbol representing the time lord, Dialga.

While he wasn't a huge fan of jewelry, he couldn't help but admire the pendent, finding the craftsmanship beautiful.

The main portion had been designed to look _exactly_ like the legend's infamous breastplate. However, instead of the familiar diamond on the front, there was a transparent one.

Inside was a working hourglass fitted inside the transparent gem, matching another that surrounded the entire piece, acting as a protective shell.

He knew it worked as he's seen it occasionally rotate, though had to be pretty close to see it do so.

At one point he asked about how it was possible, having a couple of ideas, but wanted to be sure.

Joel explained that the sand inside the hourglass was a mix of magnetic properties, the same kind also used for parts of the plate.

Using a mix of weight and what's in the sand and plate, it would rotate whenever the sand fills one side.

To ensure it would, magnets were put into the framework of the hourglass to keep it still and be attracted to the upper half. If one side is in a sense, _to_ heavy, it would be impossible until all the sand empties, thus causing it to rotate appropriately.

"What are you doing?" Sebastian asked, eyes widening when the other reached around him. "But this is…"

"I know, but I think _you_ need it more," Joel joked softly as he reattached the chain, this time around his lover. "It always gave me some strength, practically acted as a good luck charm. Hopefully, it'll act the same way for you too."

"Joel, thank you," he smiled, kissing him as the other held him close. "This is a _really_ corny gift, but I love it."

"Corny or not, I'm glad you love it."

Laughing, the older man began to feel better as they talked some more before he noticed something glinting out of the meteonite.

"Joel? What were you _doing_ to it?"

"Oh, _that_ , that happened when you came barging in," the other laughed nervously, the other blushing.

"Sorry."

"No problem," he laughed as he got up, going over to it before stopping, eyes growing wide. "This might explain the unstable energy."

"What is it?" Sebastian asked, walking up behind the other, glancing around him to see the unusual space rock.

Dark eyes widened as well, seeing a pair of glittering stones, a familiar design residing deep inside.

"Are…are those…"

"Key Stones, I don't believe it, they were embedded in this thing. I knew there was something in it; I was slowly chipping it away, but to think…"

"But _how?_ "

"I did studies; it came from a much larger one, so it must've released some energy that altered some stones nearby. As you know, there's hardly any information about where they come from or how they're created."

"That's true, but strange that there were two in there."

"You don't think it's a coincidence, do you?"

"I want to, but I get this feeling it isn't, that something is guiding us, like a puppet on strings."

"We'll hide them for now."

"Are you _insane?_ "

"Maybe, but if Giovanni finds out about these, who _knows_ what he could do with just one, let alone _two_ of them? If there's a chance someone here has a strong bond with a Pokémon that can Mega Evolve, and Dialga-forbid, possess the correct Mega Stone… I don't want to think how much stronger they'll be, what _damage_ they could cause."

"You have a point. But where could we hide them?"

"I noticed some loose tiles under the bookshelf. If it isn't some bottomless pit and no signs of a Rattata running about, we could hide them there."

"Are you sure? We could hide them with the blank stones instead. No one would think to look there than a tile. Plus I'm sure someone would notice if we kept shifting the shelf, either scuffs or having OCD about such things."

"That's true, you have a point," Joel sighed as he scratched his head. "But first things first, I have to get them out of this thing. Wherever we hide them, _it_ can't come."

"Maybe so, but how is it going to be explained?"

"Once I get them out, I'll chip around where they were to hide the fact they was something inside."

"It's risky, but could work."

"That's what I'm hoping too…"

At that, they worked together, freeing the stones from the remains of the meteonite, carefully storing them in with the blank stones.

Until they can come up with a plan or know what could be done with them, they _have_ to stay hidden.

* * *

 _ **This chapter was a bit stressful, not so much the plot, but how to make it flow. I'm still not entirely happy with it, but I can't seem to find any way to really fix it.**_

 _ **Any ideas on what could be done to improve it, either changing it up entirely, or what, I'm open to suggestions.**_

 _ **As for the Key Stones, well since they cut out the whole meteonite from the canon similarly to the GS Ball, figured it could have a different purpose. I mean, far as I know, there's no known information how Key Stones appear. There are some about Mega Stones coming from mutated evolution stones due to meteors or Xerneas/Yveltal having something to do with it.**_

 _ **If I missed something, mostly since I haven't been able to watch the series since losing cable, so I'm going by ear/eye regarding the series. That and playing the games.**_

 _ **Please read and review**_


	16. Chapter 16

_**Heads up to those who have been reading, there will be lemon, meaning, sex between two guys.**_

 _ **If you're not comfortable with it, you don't have to read, either skip it or read up to where it starts, then stop.**_

 _ **I'm not forcing you, so please don't complain about writing yaoi. It was even mentioned at the first chapter of what may occur, so you already been warned once. Just thought to give a reminder to those who might've forgotten, or simply missed it reading.**_

 _ **Other than that, enjoy.**_

* * *

Slowly things began to take shape, namely new faces appearing, apparently sent in to help with missions.

Of course, it happened shortly after Team Rocket suffered a severe blow, dozens of people and Pokémon killed. It wasn't some lab accident or an assault by Panthera or someone of her caliber.

No, it was a wild Pokémon, a powerful one.

A Mew was the cause…

Sebastian couldn't stop shaking at the news, having heard only a few survived when the Pokémon apparently committed suicide with a fatal Explosion.

Why would it even _do_ that?

What purpose did it have ending its life like that?

Unable to get it out of his mind, the various scenarios, he often slept little and times he did, he was trapped in some nightmare.

He didn't want to repeat what he saw whenever he woke screaming or simply panting hard, the screams trapped in his throat.

By how hard his heartrate went, he was surprised he didn't have cardiac arrest right then and there.

He blamed Team Rocket for all this, that Mew probably had a nest nearby and they intruded. They could have polluted the area, making it seek retribution, seeking vengeance against them.

To think Beta and Omega, Mewtwo even were all cloned from the same species…

The thought horrified him, made his heart ache knowing they could easily have ended up like that, or worse, risked knowing that devastating move.

He was such a fool for not taking better precaution that time, thanking all the gods out there they were blessed with the moves they had now.

Joel heard what happened, unable to decide whether to pity the legend who threw its life away or the Rockets that were caught in the blast.

No matter how evil you are, to die like that? It was horrible, he didn't know which was worse; hearing about it, witnessing it, or surviving it.

It made him more sorrowful when he watched his lover suffer, knowing he was scared, having nightmares himself. He simply wished there was a way to wipe those horrid thoughts from their minds, Sebastian's especially.

While he struggled to hold an icy mask in front of others, once they were alone, those walls fell apart in seconds if not faster.

He was an emotional wreck; enduring various traumas from being used, raped, losing people he cared about. It was a miracle he didn't break sooner.

If only he had a Drowzee or Munna, then it might be possible, but he didn't.

Running a hand through his sand colored hair, he gave a defeated sigh, grateful his lover began to have fewer nightmares, but still shaken.

Deciding to get up, he knew he had to find something that'd help him, willing to spend money if he had to, to get a Pokémon that'd help.

Walking steadily down the halls, he passed various rooms, mostly storage for excess gear they couldn't fit down in the second basement.

Spotting a Rocket, he caught him before he could disappear around the corner, the other jumping in surprise before giving a strange look.

"Sorry if I scared you, I wanted to ask you something."

"What is it?" the uniformed male asked, cocking a brow, crossing his arms.

"I was wondering if you might know if we have any Pokémon, like Drowzee or Munna, even their evolved forms. I want to get my hands on one if I can."

"Seriously?"

"Yeah, I've been having trouble sleeping at night and thought one could help me out. Plus I could study one to figure out some odd quirks they have, namely their dream eating habits."

"A lot of those are pretty tough to just hand out."

"I'll take whichever is considered useless; I'm not that picky about its strength, just its abilities."

"I'll take a look and see if there are any, but it isn't going to be free."

"I know, if you find one and there is no doubt of it being useful, I'll be sure to put money together or talk to Giovanni himself if need be."

"Alright then," the Rocket shrugged, heading off to check, "how do I find you?"

"I'm usually at my room, but I have others with me, and I don't want to risk disturbing them. So cafeteria would work, next week?"

"Sure."

Finalizing the time and such, they parted ways, the other heaving a sigh, finding not at all rattled with what he was doing.

In some ways he would be doing the Pokémon a _huge_ favor if he bought it than risk it getting killed or experimented on. Plus, the only thing he lied about was him having trouble sleeping. He wasn't about to embarrass his lover, letting the entire place know he's having night terrors.

No, if anyone was going to get mocked about it, it'd rather be himself, sparing his lover from further humiliation.

Unable to suppress a smirk, he stopped by a vending machine to get something to drink before returning to the room and informing the other what he did.

"You did what?" Sebastian nearly stuttered.

"You've been having so many nightmares, and while they've tapered down some, they still appear. And it isn't just you; I've had them and who knows if the girls are having nightmares, ones they're not telling us."

"So you're buying a Pokémon to help?"

"I know it's probably stupid, but if we had a Drowzee or Munna, anything that eats dreams, it might help. If I had more money and knew where to look, I'd get us all Lunar Wings to wear instead."

"Joel…"

"I know I should have talked to you about it, but it just sort of came at the moment. And spotting that Rocket? It just seemed too good an opportunity to pass up."

"I'm not mad, you made good points…. We've _all_ had nightmares, maybe even having some we're unaware of except in our sleep," Sebastian sighed as he leaned back in his chair.

For some reason, the idea was not only appealing, but relaxing, he only hoped whatever they get, whatever dreams they eat or see doesn't harm them.

He shut his eyes momentarily before opening them when feeling arms wrap around his shoulders.

Opening his eyes, looking up at the other, he gave a confused look, "Joel?"

"Sorry, just the idea of you suffering hurts. While nightmares can't physically hurt you, the emotional damage they cause…"

Pulling away, he stood up, silencing the other by kissing him deeply, the other hugging him tighter.

Nothing else needed to be said, the action enough to speak for both of them.

When they pulled away, the older man gave a soft smile, one he only shared with those closest to him.

"Despite everything that happened, there have been things in my life that are good, things I don't regret."

"Like what?" Joel asked in soft tease, burying his face into the other's shoulder.

"I met Thomas and he became the first person I could truly trust, basically becoming my best friend. If I hadn't met him, I wouldn't be here now; I'd be somewhere else doing gods-know-what. I wouldn't have joined the team and work on the girls' creation as well as raising them."

Almost playfully, he shoved the other onto the bed, having made sure he'd hit it and not the floor before climbing on top, straddling the waist.

"But what might be the best was meeting you. Not only did you become my friend, but my lover as well," he smiled as he kissed the other again. "All the good things that happened, they gave back my humanity and I'm forever thankful."

Tightening his hold over the older man, Joel pulled him closer, pressing his lips against the other, feeling hands beginning to roam.

He started to copy, hearing soft moans and gasps whenever a sensitive area was brushed or grabbed.

"Can't say I blame you," he smiled when they pulled apart for air.

"It'll be a few hours before they're due to come back…" Sebastian suddenly spoke up, making the other almost choke.

"Wait… Are-are you sure?" he asked, seeing a faint blush forming.

"I know sex isn't what makes a relationship but…but I want to know what it _really_ feels like with someone I love. With someone who won't hurt me afterwards, who will continue loving me," he answered, feeling his face beginning to heat up. "This sounded so much better in my head…"

"I understand what you're getting at," Joel smiled as he rolled themselves, pinning the other down with little effort. "If you're absolutely sure…"

"I'm sure."

Feeling there was no need to question further; the younger man began to kiss him more passionately.

Slowly clothes were removed, both getting as far as losing their coats and shirts before Joel paused briefly.

The older man was about question before crying out in surprise when a mouth began teasing a nipple, the other one taunted by a free hand.

Everything was becoming a haze, lust filling him, wanting more as Joel switch sides to tease the other before trailing kisses back to his mouth.

One hand stroked his face as the other slowly began to descend further, grabbing his belt, fumbling to get it undone with one hand.

Partly wanting to speed things up, Sebastian gave what assistance he could to get them undone, wiggling his hips to force them downward. It would've been easier if Joel pulled away, but he was far more interested kissing than getting naked, something he couldn't help but love.

He didn't think he'd _ever_ meet someone as patient as Joel, knowing it must've been partially frustrating.

The entire time they've been together, the furthest they went was a few heated make out sessions when alone. Yet they never went as far as they have how far they're _going_ to go now.

Up until now, he was scared, not of sex or Joel hurting him, but of himself, that he might not be good enough, that his rape would return and ruin everything.

But he was feeling so good now, as if _nothing_ could ruin their moment…

Another gasp escaped when the free roaming hand grasped him, slowly and gently stroke and pumping him, letting out small moans and whimpers.

He didn't think he could make such noises, but he wasn't going to complain, his lover made similar sounds if touched a certain way. And if anything, the noises they were both making were turning them on even more.

It's been so long since anyone touched him like this, even indulging himself, not since his crush on Fuji. It felt so good, feeling so close, blood rushing between his face and downwards, making him cry out when he finally came.

Panting hard, he watched as Joel gave almost a devilish smirk as he wiped his hand off before working on his own pants.

The sight alone made him hard again, feeling himself getting nervous as the other began to touch him again, but began stroking himself too.

Part of him thought the whole thing would be similar to times he had sex with Meiya, yet it wasn't. It was different, and he liked it, wanted more of it. It was becoming addictive, like a drug and he was willing to drown himself in it.

Glasses steaming from how hot he felt, he gazed hungrily at Joel as he felt himself getting close again.

"P-please," he begged, his mind spinning as he arched his back.

The way he was being touched, being kissed, it was driving him insane, his need taking its toll.

"Just wait a little longer," Joel reassured as he paused his ministrations to the other, seeing he was close to losing it.

A near whine escaped the older man, trying to buck his hips upward for more friction between them.

Joel kept him easily pinned with one hand as he easily fished through the drawer, pulling out a bottle of oil.

Getting enough on his hand, he capped it as he prepped his nearly squirming lover, unable to hide a smile on how cute he looked.

"It might hurt a little," he reassured as he faced the other, seeing his glasses were starting to fall.

He barely finished nodding before squeezing his eyes shut as a finger entered, not so much from the pain, but how strange it felt. He wasn't sure if it was hurting less due to the oil or something else, but he wasn't going to wonder too much. His body wanted to adjust, tempted between taking more or pushing away.

"Are you okay?" the other's voice echoed in the back of mind, making him pull out of his daze.

"Yes," Sebastian panted as he opened his eyes, taking note his glasses were gone.

He didn't have to look for them, knowing Joel must've taken them off for him while he adjusted. He felt his lover's hand rub his face, likely being when he removed them, wiping some of the sweat off, brushing hair out of his face.

When the finger began moving, it felt odd and hurt a little from the motion, more so when a second digit entered him. The pain slowly dissipated into blissful pleasure, making him moan and arch his back, wanting more.

"J-Joel!" he cried out, white flashing into his vision as his prostrate was struck, pleasure consuming him. "Right there!"

Heeding his words, Joel continued to stroke the spot, watching his face twisting into pleasure, face burning brightly as he threw his head back.

Leaning down, he began to trail kisses down the jawline and neck, sucking hungrily on the shoulder, leaving marks.

Sebastian might get embarrassed, maybe mad afterwards, but they weren't anywhere visible with how he dresses.

The younger man could feel hands running over, clawing at his back as he tried to have some restraint, but it kept crumbling away with each and every stroke.

"Gods, I'm close," he panted, the fingers not once stopping, unsure whether to beg for him to continue or stop before he came.

Without having to read his mind or ask, Joel smirked as he pulled the fingers out, hearing a mewling sound of displeasure.

Grabbing the oil again, opening it to coat himself, trembling hands grabbed him, nearly making him drop the bottle.

"Let me," Sebastian offered as he pried the bottle away.

With shaky hands, he began to coat his palm with it, seeing just enough to get a plentiful amount before taking hold of the other's member.

It felt so hot, swearing he could _feel_ it pulsating, the blood rushing through, not sure if he was _really_ feeling it or simply imagining it.

Maybe it's both? His body becoming so hyper sensitive it wanted to feel everything going on around him?

Joel let out a noise, almost a purr a deep purr, obviously enjoying the treatment, eyes fluttering shut.

"So good," he groaned, not wanting this to stop.

It felt so much better than his own calloused hands, or any past lover's he's had in the past. No, not lovers, they were past flings with old high school and college crushes, brief and mindless sex.

With Sebastian though, it was different, _he_ was different. He was the very definition of a lover, the thought making him smile.

Pulling himself out of the fog of his mind, he grabbed the hand stroking him, pushing him to his limits.

"This is going to hurt a lot at first," he warned, seeing some concern, "but I'll move as slow as you want. We'll go as slow as _you_ want, as _you_ feel ready."

"Joel…" the other whispered, his body threatening to tense up.

"You need to relax," the younger man spoke softly, trying to calm the other down, knowing if he's tense when he enters, it'll hurt worse.

"I-I know," Sebastian stuttered softly, taking a deep breath as he got himself to relax, the muscles loosening.

Second he gave confirmation, he cried out in pain as the other pushed in, stopping halfway when seeing his face scrunching up, the muscles tightening.

"Shh, shh…it's okay, Shi, it's okay," Joel comforted, petting his lover's hair.

Tears pricked his eyes, fighting them back, trying to ignore how much it burned, the muscles stretched farther than previously.

He was sure skin must've torn, probably bleeding, no, he shouldn't think that, or it'll just get him more stressed, even tenser than he already is. He _has_ to calm down, not just for himself, but for Joel as well.

"Move," he nearly ordered, wanting motion, calming himself down.

Joel was right, it would hurt and it did, but once he began to move, keeping it slow and steady, the pain began to dissipate, replaced with pleasure.

A loud moan came out, arching his back, legs wrapping around the other's waist as the spot was brushed again.

"There!" he cried out, clawing at the sheets as he felt his vision blurring completely in pleasure.

He could barely focus, Joel speeding up, the sounds of their sweaty bodies slapping with each thrust. The hot feeling he felt the first time he came returned with greater ferocity, the muscles around the other's member tightening.

Every time he was struck there, his prostrate rammed and teased, it felt amazing, making him shout with pleasure, panting hard.

Lips claimed his, their kisses no longer peaceful and caring, their desire and lust overwhelming, leaving them messy.

A free hand grabbed him, pumping him in time with the thrusting, making Sebastian shout when slammed into particularly hard.

Both shouted, unsure whether they were screaming each other's names or what, but what exactly they said made no impact. It was _how_ they sounded to one another, the feeling left behind that counted.

Joel came hard, filling his lover as the other came harder than previously, coating their stomachs with his seed.

Riding out their orgasms, the younger man slowly pulled out, dropping to the side of the bed, pulling the other close.

"That was amazing," Joel panted as he gave a few kisses to the other, pushing sweaty bangs out of the other's face.

He couldn't find the strength to speak, only nod as he panted, trying to put something together. But it wasn't just that, but when he pulled out, he began to fell hollow, wishing he could have stayed inside a little longer.

What finally made him gather the strength to speak was hearing what the other man said, making him almost stop breathing.

"I love you, Shi."

The way he said it, regardless how tired, how weary he sounded; the emotion behind it was there, making the other stare in shock.

"Joel…" he whispered before a smile formed, seeing the other looking at him, trying to stay awake as was he. "I love you too."

With that, it was almost a silent command to each other to sleep, the younger man numbly dragging a blanket over themselves.

* * *

 ** _Okay, I'll admit, I was a bit nervous about this chapter, mostly on how to put it out without ruining it, but figured I'll do my best and if I did make mistakes, someone will be mention it and give some friendly advice on how to improve it._**

 ** _Now for the reason for adding a lemon, sure it may not be entirely necessary, but at the same time it sort of is as a growth factor. If you recall earlier chapters, the professor wasn't exactly easy to let others in, more so after being assaulted. Sure, I don't know much about rape victims, at least male ones, I can only guess, plus add in their own individual personalities than the stereotypes put on such victims._**

 ** _So yeah, wanted this as a means of showing how far he's gone in healing to let someone in that intimately, the sheer amount of trust put in to let those walls down._**

 ** _I hope that made some sense..._**

 ** _Please read and review_**


	17. Chapter 17

Since that night, the two felt closer than ever, some of the other Rockets taking notice by how much happier the older man looked.

Even the clones noticed the change, the younger one having an idea from the various books she read, but unlike her sister, kept it to herself. They don't need to be embarrassed being found out of their private activities. There _is_ a reason the term _private_ is used, especially in situations such as these.

But there was one thing bugging the clone as much as it was bugging her sister, waiting for an opportune moment.

It eventually came when they were in their usual spot in the cafeteria, Joel having run over to meet with some Rocket before returning, grinning like a fool.

"Our latest addition?" Sebastian teased when the other sat down, the clones curious at the Pokéball.

"Yup, was told that despite is rarity, it was really weak and most wouldn't bother buying it. While most want a trophy Pokémon, they also want one that can fight if they needed it too. Still cost me quite a bit, but I think he'll be worth it," he explained as he decided to call it out.

From the ball, surprisingly enough a shiny Munna appeared, looking confused, scared even before gentle arms wrapped around its pudgy body.

"There, there now, you're safe with us. No one's going to hurt you," Joel comforted as he petted the Pokémon gently.

"Muun?" it whimpered softly, glancing up at the kind face before focusing on the others sitting around the man.

 **"** **What is that?"** Beta asked as she looked at the nervous Pokémon.

"This is a Munna, a psychic type native to Unova," Joel answered with a smile.

 **"** **Unova? What's that?"**

"A region far from here, it has a lot of technological advances we're using today, such as the recent development of reusing TMs much like the HM disks and drives," Sebastian answered with a smile as he watched the older clone listen.

Whether she kept full attention or not to his explanation, it was still fun to teach her something new, knowing in the back of her mind, the information would stick.

 **"** **Professor, could I ask you something?"** Omega spoke up, almost nervously by the way she shifted in her seat, eyes downcast with worry.

"What is it?" the older man asked, placing a gentle hand on her back to comfort her, worried of what might be bothering the Pokémon.

 **"** **Why** ** _are_** **we training so hard? We get stronger and stronger, but it doesn't seem to be enough. And there are talks of going after someone, is that why we're training? To hurt someone?"**

He should've known this would come up at some point, and it made his heart ache having to tell them. But it seems it's as good a time as any, he just hoped neither will hate him or Joel for not telling them sooner.

"I'm afraid so," he answered bitterly, unable to look either one in the eye, Joel gazing at the floor.

 **"** **Is this person bad?"** Beta asked, almost hopeful.

"N-no…"

 **"** **Then we're bad?"**

"No!" Sebastian almost shouted, eyes alarmed. "No, you and Omega are _not_ bad. Not at all, and never will. It's who's controlling you, telling you what to do…"

 **"** **Are** ** _you_** **bad? You tell us what to do when we train and you're free from working on your researches."**

"I've…I've done questionable things…"

 **"** **You're not bad, and neither is Joel,"** Omega spoke up, making their heads turn to her determined face. **"You may have done** ** _bad_** **things, but you're not bad. I can't explain it, but I just know it, neither of you are bad."**

"Omega," the younger man whispered.

 **"** **Can't we just leave? I don't wanna be with bad people. I don't want** ** _any_** **of us to be with bad people,"** Beta whimpered, tears forming in her eyes.

"I've thought about it, but Giovanni won't let us go that easily. He would hunt us down, bring us back here, maybe even hurt us… _kill_ us if necessary."

He hated sounding like this, having to tell the clones this, seeing how shook up they both looked, the older one more so. He swore he could hear their hearts breaking into millions of pieces along with his own.

 **"** **So we're stuck?"** Beta softly cried, tears starting to fall down her sweet face.

Reaching over with a napkin, wiping her face dry, he gave her a saddened look before speaking, "I wish there was a way for us to get out of here, for you two to leave safely. But until then, we need to make due. It's the only way we can survive…"

 **"** **Our brother… He isn't on a vacation, is he?"** Omega asked, tears threatening to spill, but held together better.

"No, unlike us, luck was on his side and he managed to escape twice. On his second escape, he wiped a lot of memories, so no one remembers him. Those who evaded that were Joel and I, Hun even. Tyson somehow remembered, though it's still mostly fuzzy to him in some parts."

 **"** **I wish we could leave,"** Beta whimpered softly, flopping her head down on the table, now pouting. **"So many are mean here. I don't like them. I wanna be able to go outside and play again. I wanna be able to finally play with Uncle Tyson. I want to meet Uncle Hun and Uncle Attila and play with them too."**

"I know, sweetheart, I know," Sebastian sighed, feeling guilty for how upset they both looked.

Joel was right, they _have_ to get out of here, and seeing just how upset the girls were, he had to find a way.

He didn't care what happened to him, he just wanted to get them and Joel out of here, and if he's lucky in locating them, get his daughters out of here as well.

Maybe get the others too if he's _really_ lucky?

Tyson is obviously questioning his loyalties since Giovanni shut that tank down, destroying what was left of Amber. And there's Hun, possibly Attila too from the brief time he got to know him. But the pair were still missing, no word about whether they're runaways or on a secret mission.

This place is going to end up being their tomb, damning their souls if they stayed any longer.

But how could they escape?

How could they avoid getting killed, evade agents left and right?

Their best bet would be to find Panthera, knowing _she_ may be the only means of surviving. But how do they locate someone like her?

Even if they did know where she is or who to go to that could lead them to her or bring her to them, they still have no idea how to escape.

An idea suddenly popped into his head, glancing at Joel, seeing a similar glint shining in his eyes as well.

"Beta, Omega, I know it's sudden, but care to help with an experiment?" he asked, glancing at the younger twin, hoping she'll get it.

And with that hope, a light shined, eagerly nodding, her sister unsure what was going on before the two chattered in their native tongue.

Lighting up, she sat straighter; tail beginning to wag much like an excited Herdier earning itself a treat.

If what he has in mind ends up working, then they _might_ be on the road to leaving this place finally.

Returning to their room, Joel grabbed the box carrying the key stones and blanks, sitting on the bed alongside his lover.

The Munna had been returned for its safety, seeing it was rather timid, not wanting to scare it by accident.

 **"** **What are those?"** Omega asked when the box was opened, revealing the stones.

"You remember what Joel and I had been working on?"

 **"** **Mega Evolution?"**

"Correct, these two stones are known as key stones. We _just_ found them not that long ago. As for these, we've had them for quite a while, before you were born. They're known as blanks, having unstable energy, no focus on what a Pokémon could Mega Evolve into. At least not until it makes contact _with_ a Pokémon to change them if they're lucky enough."

 **"** **You want us to touch those stones then?"**

"In a sense, yes, but it isn't that easy. It would have to be done while performing attacks," Joel spoke up.

 **"** **But you don't want others to know though, right?"**

"That's correct," Sebastian answered as the two clones took a stone. "I'm not sure exactly how we can work it without Giovanni or anyone finding out."

 **"** **Couldn't we use weaker forms of our attacks? We've been practicing a lot,"** Beta suggested, making both men do a double take looking at her.

While she wasn't dumb, it was rare for her to come out with something like that, let alone something that actually _could_ work.

"It could very well work…" he whispered as he stared at the stones. "We'll try it, but before we do, we need to make proper holsters for you two as well as ourselves."

 **"** **How come?"**

"It'd be easier for you to fight until you can Mega Evolve without having to worry about dropping it," Joel explained.

To make it easier, he pulled out various photos of other Pokémon capable of Mega Evolution, showing the before and after.

 **"** **I think I get it…"** Omega muttered as she studied the photos.

"But it would have to be subtle, to avoid being caught."

 **"** **Like hiding in plain sight?"**

"Exactly," Sebastian smiled.

From there, the four worked out various ideas on how the key stones could be worn, knowing they would have to be somewhat visible, yet easy to hide. Afterwards, they would work on the girls, silently hoping this experiment works.

As they worked, they waited for opportunities to train the girls in secret with the blank stones to activate them.

However, no such luck came, leaving them growing somewhat desperate, but held together, reminding themselves what was at stake.

Between that, Sebastian continued to do his research on Panthera with more vigor, making various notes.

One set would go to Giovanni as per usual, the other being for himself in hopes of finding out where the woman may be or how to contact her.

"Any luck?" Joel asked, setting a cup of coffee next to the other, leaning over the notes. "Damn, how much _is_ there on this woman? I feel like I'm reading a history book."

" _A lot_ apparently, but I think I have an idea how to get to her," Sebastian sighed as he stored his secret research away.

"Really?"

"Yes, but it isn't going to be easy," he sighed, taking a sip of the bitter drink, staring at his reflection. "She started her Pokémon journey in Pallet Town, receiving her first Pokémon, a blind Pichu, from Professor Samuel Oak."

"You think he might know?"

"I can't guarantee it, but fact she keeps going to new regions; she may have very likely talked with each region's professor or any with much influence. If Oak doesn't know her location or know a way to call her, then one of the others might."

"I get it, but how do we even _get_ to him? Not like we can just take a drive over to his lab, not with Giovanni hovering us."

"No, we would have to find a way to escape and be on the run, maybe even fake our deaths and loop around to reach him. But being there are more demons appearing and who knows what else, _that_ might make it harder."

"That's true, more so if we still can't get the girls to use the stones."

"They _have_ gotten stronger, but Giovanni is stronger and who knows what else is here or may come if we tried to run now. I don't even know if having them Mega Evolve is even possible, let alone make them strong enough."

"Even if they aren't strong enough, it might pose enough of a distraction to give us time to escape. I still have Kadabra, I can have him teleport us to safety. Thing is…"

"What?"

"I know it's tough to think about, but we may have to think about _actually_ capturing Beta and Omega in Pokéballs."

"Are you insane?"

"Listen to me, Shi and think about it. Whatever we do, it's going to be absolute chaos, I'm sure of it. I'm confident Kadabra could very well get us out of here with a Teleport, but not if we're separated. If the two of us and whoever we can get to come with us are together, any Pokémon we have out fighting can be recalled."

"But to put them in Pokéballs though…"

"I know, love, but it doesn't have to be permanent. Once we're safe, confident we've escaped, we can release them and if necessary, destroy the balls."

"You're right, they _are_ Pokémon, it would be logical. They aren't human, no matter how much they act it, how we may treat them."

"I know," Joel comforted, hugging the other. "I'll try to get a couple of empty balls, you have a trainer card?"

"I do, I haven't used it in a long time though. Up until they were born, I never raised a Pokémon personally. I only got the card, re-registering when I can for research purposes, in case I _had_ to catch a Pokémon for some reason."

"I think this counts as a good reason."

"It does," he smiled, leaning over to kiss the younger man before returning to his notes once again.

* * *

 _ **To me at least, it feels a bit short, but I didn't want to drag it on for to long.**_

 _ **But yes, seems a plan is starting to form, now to see if it actually takes fruition or not...**_

 _ **Please read and review**_


	18. Chapter 18

_**I apologize for the delay posting this, things got crazy at home as well as having had to somewhat scramble to finish the next chapter.  
**_

 _ **So without further delay...**_

* * *

Weeks passed as Sebastian continued studying the names of Panthera's kin, trying to decipher the ancient language.

It was something most would have difficulty to understand even the basic alphabet, yet _somehow_ he was learning.

He doubted he's getting everything right, but as things began to piece together, it was starting to get easier. It was now taking less time than waiting for another to translate and give back to go over.

Not that he'd ever tell Giovanni or anyone else about what he's been doing between reading Panthera's files. He's keeping this hidden, only Joel and the clones knowing about it. He didn't need more papers dumped on him or made to move to work translating more documents and papers.

The only drawback to all this though was the more he understood, the closer he was to identifying who Panthera's kin are.

And he wasn't sure what to do if that were to ever happen…

"No…" he whispered loud enough for his lover to hear him, running over when seeing how pale he was becoming.

"What's wrong?"

"I…I think I found one of her children," he answered, unsure whether to rejoice or quake in fear.

Scanning the research, seeing how hard his lover has been working trying to understand a language he didn't even know existed.

He glanced the names over, seeing the older man has been comparing them with names of those living in their world. Thankfully there was _some_ detail of what they looked like to help narrow things down to avoid spotting multiple names.

"Holy… _Lance_ is one of her kids?" Joel nearly shouted, re-reading the information translated and studied over. "If this is real, why hasn't he shown any signs of being this Cateron?"

"He was reincarnated into that family, bearing no memories," Sebastian sighed, rubbing his hand over his face.

"What do you mean?"

"Panthera used a spell to seal everyone's memories off due to an age reversal spell she attempted to use, but lost control over. She likely did it to spare them emotional trauma if there was any chance of them recalling their previous life."

"Why the hell would she do that?"

"Their planet was dying, what else was she supposed to do? What would you and I have done if forced in her position?"

"You're right… Sorry," he apologized, taking a deep breath, "but what should we do though? We can't just tell Giovanni, but not try and make contact with this guy. At some point they'll figure it out…"

" _If_ they don't already know," he sighed, "even if Giovanni _himself_ doesn't know, Darkness may know, but keeping it silent, wanting to find more. She doesn't just want Panthera dead, but her entire family as well."

"That's right… But why would she be so desperate having them all killed though? Especially if they don't even remember?"

"I don't know. I honestly don't know…"

Feeling the other hug him, trying to bring comfort, it helped him calm down a bit, yet his mind was still a raging storm of confusion.

"But if he really is one of her kids, if he has no memory, why didn't she restore it when they've obviously met? Why let him remain unaware?"

"She likely didn't know the full danger she was in, let alone her entire family and any others from their world. She likely didn't need to stress him out, leave him confused, maybe even torn between loyalties between his reincarnated family and real one."

"That makes sense, but she likely would be gearing up to do so if she found out Darkness is here, at least her presence."

"Quite likely, but she would need to plan it and may be searching for any others here as well. She could be using the whole trainer thing as a cover to find them without drawing attention and travel safer than relying on her abilities alone."

"But to think the champion for Kanto and Johto is one of her kids…"

"I'm not that surprised, while I've yet to translate all of these papers, fact she was a queen on their world, he likely held a similar high position. Same with any of her other children, each bearing a unique talent to support not only each other but those they called their friends as well."

Heaving a small sigh, he put what he found aside, unwilling to reveal what he's learned, least not right away.

Being this is Lance, not only champion of the Pokémon League, but part of the G-Men, he was _very_ well known. If he suddenly disappeared, not only would it draw Panthera in, but dozens others as well.

Other champions, gym leaders, officials, members of his clan… If he revealed this information and it happened, it would be a bloodbath. Worse, the man would be completely unaware of why this happened, not knowing why he was kidnapped, at least not the real reason.

After a few days, it began to get pushed to the back of his mind, slowly finding more names that matched to residents of this world.

Some were gym leaders, others various people who've made it on TV participating in contests or leagues, sometimes both.

Then there were others that had criminal records, one of them going missing, the same man who nearly ended the world trying to capture the legendary birds. Being he's gone into hiding or simply vanished for unknown circumstances, there wasn't much he could do even if he _did_ hand it in.

But the other criminal he found…

Sebastian had walked into the cafeteria, aiming to get some coffee, tired eyes glancing at the one person who could very well draw Panthera in like a moth to a flame.

While she loves all her family, he's certain of it, there were some members she would be extra protective over due to their roles and abilities.

Butch was one of them, spotting him sitting with his partner, their Pokémon out to eat than forced into their Pokéballs.

Ever since they returned from that failed mission regarding Mew, having failed to acquire the egg from what he's heard, they seemed _different_ …

They weren't as cocky and sure of themselves, the man especially. They were kinder to their Pokémon, obvious by how more affectionate said Pokémon were to their respective trainers.

To think someone like him was not only one of Panthera's kittens, but if he read the translated documents correctly, he was supposed to be the heir to the Caterian throne.

 _His_ role in the family is greatest, meaning Panthera would very likely do almost _anything_ to keep him alive. Planet or no planet, they're still royalty; still have those from their world to lead now that memories needed to be restored.

He _can't_ let Darkness have him, use him as bait or a possible weapon against Panthera; he _needs_ to get Butch out of here. But how?

How willing are they to leave?

To abandon everything they've worked for in Team Rocket?

And where could they go without being followed?

The professor nearly leapt out of his skin when something grabbed his arm, turning to see Omega, having come to find him.

 **"** **Professor? Is something wrong?"** she asked, concern echoing off her words.

"I'm not sure," he admitted, feeling somewhat comfortable talking about these things around her as he would Joel.

 **"** **Is it because of them?"**

Seeing her subtly gesture to the pair he was watching, he gave her a nod as they sat somewhat far to avoid eyes as they quietly talked.

 **"** **If I may ask, why?"**

"See that man? I've come to learn he's very special, precious even to Panthera, but I'm not sure what to do. I can't tell him, he likely won't believe me. And even if he did, what could he do? He can't simply leave and I don't know if he even wants to. While he likely had a good heart in his old life, doesn't mean he still has it."

 **"** **But he does,"** she stated, making him eye her unsurely. **"He does have a good heart. Why else would he have that baby Mew with him?"**

"What? What Mew?" he asked, trying to keep his voice low as he glanced at the Pokémon, trying to spot what she claimed was the legend.

 **"** **She's not out, but I can smell her on him."**

"How long has he had this Mew?"

 **"** **Since he came back in that cast."**

 _"_ _So he and Cassidy_ did _find the egg, but lied about it,"_ he gasped in his thoughts, realizing he might have hope.

Even with this knowledge, how could he approach them without drawing attention to any of them?

Spotting Cassidy's Sableye, an idea already began to churn in his head, praying it won't backfire as he rose, forgoing coffee. What he has planned was more than enough to not only wake him up, but focus his mind too.

He heard Omega following close behind, the pair reaching the two Rockets just as they looked up.

"Professor?" Butch questioned, appearing nervous, but retained a cool disposition, but his eyes gave his emotions away.

"I'd like to talk with you two privately," he stated, trying to keep a neutral tone, feeling as if eyes were on him than those his attention was on. "Follow me, please."

The two glanced at one another before returning their Pokémon, throwing whatever they didn't eat away as they left together.

"Professor Sebastian is it? Why do you want to speak with us?" Cassidy asked nervously, showing her voice as much as her eyes.

"You'll know shortly, I simply didn't want someone listening and butting in," he half lied as they trekked back to his room.

It was the only place he felt was safe, almost a sanctuary with who occupies it aside himself. But he had to be careful with it, one wrong move and it could be destroyed, ruining everything they've been working on.

Arriving, he opened the door, gesturing them to walk inside, noting the confused looks on Joel and Beta's faces.

The former was reading while the other batted a ball around she found in a box, which was quite amusing for someone as big as her acting like a newborn still.

"Shi… Professor Sebastian, what's going on?" Joel asked, almost cursing himself for speaking his lover's name freely.

Shutting the door, he gave a small sigh, "Joel, that Munna you got, does it know Safeguard or a similar move?"

Realizing what he meant, he nodded as he called out the Pokémon, having it perform the move, making it so nothing they said could be listened in.

Relaxing, the older man gave the confused Rockets a smile as he gestured a couple of chairs as he sat down next to his lover.

"I need you two hear me out, no questions, just hear me out," he started before either could start questioning.

Both glanced at one another, obviously unsure, but slowly nodded.

"You two need to find a way to leave Team Rocket immediately," the professor stated, making the others stare in shock of his boldness. "And it isn't just the Mew you have hiding with you."

"Wh-what Mew?"

"Omega and Beta are _clones_ from a Mew; they have similar scents and Omega happened to pick yours up. I didn't know until now when she mentioned it, thus leading us here among _other_ issues that have come up."

"Mention? You mean you can _understand_ what they say?"

"Telepathically," he smiled, the clones appearing very proud, albeit still confused, the older twin especially. "But that is something else and compared to what I've found, not important."

"Why do you want us to leave?" Butch asked, feeling his heart starting to hammer in his chest as he unconsciously gripped his pants.

"It's more _you_ have to leave. Cassidy _could_ stay, but being you two are partners and likely close, Giovanni may hurt her to find you if not lure you back."

He could see the colors on their faces drain, still unsure, but not liking where it was going, the younger man especially.

"Why though?"

"You've heard of Caitlin Panthera?"

"Of course, she's not only the multi-regional champion, but one of the few people to take on Team Rocket singlehandedly."

"And do you know why? Or more precise, _how_ she can do it?"

"Are you saying she isn't human?"

"That's correct."

"What does this have to do with me?"

"I've been given the task of finding her, using my paternal instincts to try and think like her and locate who her children may be. But there's more to it, these children have no recollection of her or who they really are other than name."

Before either could ask more, he took the chance getting up, pulling out what he could find, showing them, saving one part for later.

"So she lived on another world, but it destroyed itself, forcing her to use some spell to save hundreds, including family and close friends?" Butch muttered as he read the papers, his hands shaking. "But what does it have to do with me?"

"Believe it or not, you're part of that family to," Sebastian stated as he handed his most recent findings, letting the much younger man read them over.

Coppery eyes grew wide, the papers dropping as his hands shook, torn between laughing at the absurdity and screaming.

But screaming for what reason though?

Fear? Confusion? Anger? Sorrow? Guilt?

"It can't be true; there could be another guy with the same name that looks like me, right? That can happen, right?"

"Yes, it can, but…" Sebastian whispered, seeing how upset the other looked, starting to regret bringing them in. "But from what I've found, there's no other that looks like you. Same names, but they don't _look_ like you."

Cassidy placed a hand gently on the other's shoulder, seeing how torn her friend looked since the mission with Mew.

"Butch, whether it's true or not, this just gives us more reasons to leave. They could use you as bait, possibly _kill_ you because of the relation, regardless if you were loyal or not."

"Where could we go though?" he muttered, burying his face into his hands, looking like he was ready to be sick, not that anyone could blame him.

"I've read more on Panthera and she is associated with the G-Men. If you two can somehow get to the Pokémon League or bring someone from there associated with them, they may be able to contact her somehow."

"We thought the same thing, but there are a lot of guards who work at the Pokémon League who work for Team Rocket. It'd be almost impossible to sneak in without having them find out we aren't meant to be there."

"But Professor Oak might be able to bring someone like Lance in," Butch spoke up nervously.

He remembered the name in the papers, realizing they may be brothers from another life, technically _still_ brothers.

The whole idea was ridiculous, yet how could he really argue without doing some DNA test and that's impossible without having Panthera's DNA.

There's a chance his could match or have enough similarities with Lance, but who knows, they were born in two completely separate families. That part of their bloodline could be thinned if it even exists still.

If it exists at all…

Mentally shaking his head, he looked up, seeing how distraught his partner looked, how sad the scientists looked, the older one especially.

It was clear he was torn about telling him, but the fact he's got the baby Mew, kept it hidden from Giovanni, it was as if he felt it'd be safe to do so.

Hesitantly, he pulled out the hidden ball, glancing at it, the baby Pokémon likely slumbering inside.

Not taking his eyes off the ball, he decided to ask, _needed_ to ask, "Why? Why are you telling me? Not taking this to Giovanni or some other higher up?"

"I could ask the same thing regarding Mew, but I think we _both_ know the answer to that one."

"Giovanni's basically lost it. He isn't the same man who hired us, who gave us our missions. I don't know if what happened in Unova did it or something else, but we can't stay here."

Gripping the ball, he squeezed his eyes shut, realizing what they were talking about, if it was found out, they could all end up dead.

"How do we escape though?" Cassidy asked, partially to draw their attention away from whatever they were thinking about and focus on something important.

"I haven't figured it out, but I have some plans, but it'll take time, at least for us. For you two, the best I could think of would be to try and find some excuse to attack the lab or maybe even a gym and get help that way."

"I've heard they put up a new museum in Pewter City, finally tearing down the old one to be up to code. Maybe we could try to _sneak_ in and steal some fossils, but get caught along the way," Butch half joked, knowing such a plan would hold to many flaws.

While they've made mistakes in the past, something like this, and in a town like Pewter City, not even the bumbling trio could screw up. The location and job itself was too damn easy, suited more for newbies than people like them.

"I'm sure you'll think of something if not we might, which we could have Omega or Beta inform you telepathically."

"What about you two though? Aren't you going to escape?"

"We do, but…"

"But what?"

"I can't leave," Sebastian sighed, feeling fingers intertwining with his. "Giovanni is using my daughters as leverage to keep me here. Even if I did escape, he'd likely punish them to get back at me."

"Tell us how old they are and their names? Maybe we could find them and let you know how they're doing? Unless they're scientists, the two of us are likely to run into them or hear more than you would."

Surprised at the offer, the man gave a soft smile, "Thank you."

* * *

 _ **Now things are getting interesting, not only is the professor and Joel plotting on escaping, but have two others joining them. But will they succeed or fail?**_

 _ **Please read and review**_


	19. Chapter 19

It wasn't easy, but within a couple of weeks Butch and Cassidy were able to find out more about the professor's daughters.

They told him how they were doing, confirming that the reports given _are_ accurate and up to date, relieving him of some worry.

However, what the reports left out was _what_ they did, and when reading how ruthless and cruel they are, the older sister especially, it made him feel ill.

Thanks to their digging, he learned that after they came of age after training, they became more hired hands than actual agents.

At some point they were arrested, but Giovanni bailed them out shortly after, exactly _how_ it was done, he wasn't sure and didn't care to learn.

But due to that, now they're working full time for the Rocket leader, neither of the girls aware that they're being used to keep their father in check.

If things had been different, he probably would have been proud of their achievements, hearing how they captured several legendary Pokémon. While a few managed to escape, it hardly caused a dent in what they usually obtained to receive a severe lashing.

But now it simply made him depressed, unsure if he could bring himself to even _talk_ to his daughters if given the chance.

Aside the difficulty it would bring between their ranks higher than his and the fact Giovanni would do everything to keep them apart, what _could_ he say to them?

How could he convince them to leave this if they accept it as normal?

Would they trust his words if he told them their lives are on the line because of their relation to one another?

Would they turn him in if they learned of his eventual betrayal?

Would they even _recognize_ him as their father?

The more negative thoughts entered his mind, the worse he felt, the clones and Joel having little effect on cheering him up. Not even Butch and Cassidy could help comfort him whenever they visited.

While he knew it was a huge risk to involve his daughters, not knowing if they could be saved, he simply couldn't abandon them.

Whether they're aware of the situation or not, if he left, Giovanni could do something to them and make sure he knew it. He wouldn't be able to ever forgive himself if they were hurt because of him…

So distracted in his thoughts, he nearly leapt out of his skin when a hand landed on his shoulder, spinning to see Joel standing there.

"You'll think of something, I'm sure of it," he reassured, knowing exactly what was going through his lover's mind.

He didn't blame nor hate him worrying so much, just as he got so close to reuniting with his daughters; more obstacles appeared, now having to work around them.

"I can't simply call them up, Giovanni may find out or worse, they _tell_ that bastard and he does something to me or them, or any of you!"

"Maybe we could find a way where we need them for a job?"

"What?"

"I can't say I like this idea, but there _are_ some museums that showcase very rare fossils of actual mega evolved Pokémon such as Aerodactyl. For those to remain even after death would have serious scientific value as well as monetary value."

"But something like that would heavily guarded though…"

"And based on their reports, they may be the best for the job or at least to survey and report back to us and whoever may be more able to handle it."

"Even if it's possible, Giovanni wouldn't risk them meeting me. He'd either send you in hopes you don't know who they are or threaten us _not_ to speak with them about anything _other_ than the job. Or simply use a third party to report between us, making it harder if not impossible to speak with them privately."

"We do have Butch and Cassidy on our side, so we could use them if that option was made available," he added, seeing the other still look unconvinced.

Before Sebastian knew it, Joel grabbed his arm, pulling him to his feet and hugging him close, letting him rest his head on his shoulder.

"We'll find a way, I promise you," he reassured, planting a soft kiss on his lips.

 **"We could try talking to them,"** Omega offered, both men snapping their heads in her and Beta's direction. **"We could make it seem like a dream if we borrow Munna and his Dream Mist."**

"That could work too…" Joel started before the other interrupted.

"It's too risky to try," Sebastian stated solemnly, knowing they'll wonder why. "Given their training and ranks, I doubt they'd think it was a dream, especially if both have it or the wrong things are said in the dreams. And even if they did, they're likely to report to Giovanni and he'd find out for sure."

Second he said that, the others felt the colors drain, realizing he was right, the clones looking sadder than before.

The older scientist gave the two a soft look, the younger clone especially before speaking, "I just wouldn't know what to do if he found out you could communicate telepathically. Who knows what he could use you two for, or…"

He stopped before he could say anything else that might scare the poor Pokémon, feeling his own hands shaking.

"I'm sorry," he whispered, hanging his head.

 **"Don't be sorry. You're trying to think for all of us,"** Beta reassured as she leaned into his chest, a low rumbling purr escaping. **"But I think Omega's right. We don't _have_ to see them in person, just know what they look like and try to connect with them elsewhere."**

"Even if we did, how would you two be certain you synced with their minds?"

At that, the clones' tails drooped, the younger one's especially, clearly having not thought that far, not that the man could blame her. It isn't easy for her to enjoy reading as much as she used to. With Giovanni hovering over them, if he were to find out, it could cause serious problems for all of them.

A Pokémon that can read would be dangerous in his view, as _that_ Pokémon would get ideas and plan. The talking Meowth is a good example, though unlike Omega, he's rather gullible, so isn't likely to betray Team Rocket any time soon.

If he knew or knew how well read she is, who _knows_ what he'd do to them, do to her most of all.

Sebastian barely suppressed a shudder at the awful thoughts running in his mind, glancing at the clones, seeing how upset they were.

"Beta… Omega… I'm sorry for shooting that idea down. It really is a brilliant plan, but if we went ahead with it right now, the chance of being found out is just too high. We may use it, but we'd have to bide our time and find the right opportunity."

 **"Of course,"** the younger clone smiled, her voice sounding hurt, but as always, completely understanding.

For a while, they four sat and talked, managing to divert the conversation to something more pleasant.

Before long, they were in a better mood, more so for when they had to leave to get food, not needing to draw unnecessary attention.

Sitting at their familiar table, they gave a subtle wave towards Butch and Cassidy, needing to keep a bit of a low profile.

They managed to avoid too much issues, namely due to Attila and Hun still missing, the professor had no one to help with the mega evolution tests.

However, due to Cassidy having Sableye and a corresponding mega stone in storage to be either used or sold. All they missed was a key stone, which _they_ somehow acquired, though neither told them _where_ they found it.

The chance it was stolen is likely, but the way they acted didn't seem so, so maybe they simply got really lucky finding one or having it given to them.

Either way, whenever they came by, Cassidy mostly, it would be in a gym to help her practice controlling Sableye's increased power.

To say the least, it was difficult, the dark type often needing to be restrained or knocked unconscious with a strong Hypnosis shortly into training. But they were determined and slowly began to master it. And with it, it allowed the two scientists to study how they worked as well as study Sableye in its mega evolved form.

Taking their seats, they began to eat before the crackle of the loud speaker came, making them pause as did everyone else.

 ** _'Everyone is to report in the main hall in ten minutes,'_** the intercom echoed loudly, making several murmur.

"Wonder what that's all about?" Joel muttered as he cautiously ate as did the others, the eldest feeling his stomach twist, forcing him to stop. "You okay?"

"Not sure, I just get a bad feeling…"

The younger man gave a soft look, willing to take a risk as he clasped his hand over Sebastian's giving it a reassuring squeeze.

"Whatever it is, we won't let it tear us apart."

"Thank you."

Managing to resume eating, they got their fill before heading out with everyone else when it was time.

As they made their way, the clones kept close to them and each other, even grabbing their arms out of nervousness.

Stepping into the large room kept solely for holding large meetings, usually if it's relating to a mission that'd require a lot of bodies.

It sort of reminded Sebastian when so many were sent out to Unova and likely the same thing done back when they were hunting down Mewtwo.

Thinking about the Pokémon made him worry, what would happen if he got spotted by a Rocket? Even if a low rank doesn't recognize it, Giovanni would if he compared it to the clones. He'd wonder and likely become infuriated if he found out he and Joel knew all this time and never said a word.

The thought made him shudder, praying to all the gods that Mewtwo hasn't been found and never will be for everyone's sakes.

Glancing about the large room, he nearly broke down when seeing two young women, the very same from the info Butch and Cassidy gathered.

"A-Annie… Oakley…" he stuttered softly, thankfully the clones and Joel hearing him, the rest to immersed in their own conversations.

"What is it?" Joel asked, worried for him when seeing how distraught he looked.

"My…my daughters, over there, they're here…" he nearly whimpered, torn between joy and fear.

The younger man looked over, seeing where his lover looked as did the clones, looking at the young women.

 **"They look scary…"** Beta softly whimpered in their minds.

Sebastian glanced between them, mostly Omega, the other already understanding, as she already aimed to sync into the women's minds without their or anyone's knowing.

Once done, she would later share what she learned so her sister could do the same, knowing she likely would have unknowingly made a scene if she tried now.

The professor, despite his shock seeing his daughters in the flesh, he couldn't help but admire how amazing the psychic twins are.

One would almost think the older one would grow jealous that her sister could do so much more far better than herself, yet she didn't.

He had to admire her, knowing if she wasn't so sweet and kindhearted, she likely would have become cynical and constantly jealous. The same can be said for Omega, for not flaunting her talents in front of her older sister, always modest, but in a way that any would admire.

Lost in his private thoughts, he nearly jumped when one of the numerous grunts bumped into him, muttering a quick apology.

Before he could think of saying something, the room went into a deafening silence, making his blood freeze where he instinctively grabbed Joel's hand.

A reassuring squeeze was all that took to keep him in check as the two and hundreds others looked up at Giovanni.

At one side was his assistant, Matori, and on the other was the man's Persian, though the scientist had to note it looked a little on the depressed side.

Before he could dwell on any thoughts regarding the cat's strange behavior, the Rocket leader grabbed everyone's attention.

"I'm sure you're wondering what I brought you here for," the man spoke, others silently agreeing, too nervous if not downright terrified to speak their minds.

He cast a glance at Matori who held a remote, having a screen drop down, the lights dimming, nearly shrouding all of them in darkness.

Sebastian felt himself shiver, getting a _really_ bad feeling in the pit of his stomach just as the remote was clicked again.

Immediately, the image of the infamous trainer, Caitlin Panthera was shown, the scientist remembering it from one of the many articles he read about her.

She was smiling happily, a Weedle on her shoulder looking just as happy as her.

"I've just been informed that Panthera's been sighted at a rather _unique_ and famous city, having been staying there for some time."

"She's been found?" Sebastian muttered under his breath, giving Joel and the clones a worried look as did they.

Another click and what looked like a floating island appeared from a distance, Giovanni explaining the city was known as The City of Legends.

It gained this name due to having a very extensive library on the history of not only Pokémon, but demons as well. It is also known as the Wandering City; thousands of Float Stones attached to make the city hover hundreds of feet in the air.

"We will surround the city in exactly three months where it will have reached _this_ location," the leader explained as a map was shown of the city's pattern based on its previous travels. "It is isolated enough to avoid _unnecessary_ interruptions."

He paused, clearly eager to tell more, like a child who just did well in school, wanting to show off and be rewarded.

Murmurs rang through the room, various members talking amongst each other, realizing their organization's top enemy will soon be eliminated.

Once it died down, the man continued, "However, we will not be alone as I've come to learn that Ms. Panthera is _far_ from normal. She happens to not only be an enemy of Team Rocket, but an enemy to others as well, who wish her dead as much as we do. Not only that, but she has apparently called a secret meeting with nearly all the gym leaders and members of the League."

At this, Sebastian felt his eyes widen, wondering if that's how the woman was found, having not known the Rocket leader was also the gym leader.

"What sort of meeting you're wondering? To be honest I'm curious too, so I'll be attending, to scout out and report."

At this, the more devote members risked speaking up out of worry of their precious and insane leader.

"Giovanni, Sir, isn't that dangerous? What if Panthera finds out who you really are? Or any of the other gym leaders and elites?"

Giving almost a sympathetic smile, he instantly reassured the worried Rockets, "There won't be any worry. I have an _acquaintance_ that will ensure I'm not found out. Hence the three months, it will be used to find out what she is planning in case it has any effect on ours. If it does, I'll report so we may make necessary changes. If it doesn't, then we proceed in destroying Panthera."

"And her Pokémon?"

"They're far too loyal; my _acquaintance_ is actually planning a full scale assault on the locations where she keeps her unused Pokémon. So I would _highly_ recommend that if any have Pokémon that may be there, have some _special_ connection to you or to someone you know, I suggest you get them now before it's too late."

Sebastian felt his blood run cold, realizing Giovanni must be talking about this Eclipse if not Darkness.

Those women, those _demons_ , are going to slaughter hundreds of innocent Pokémon! And worse, if what he's saying is true, then that means not just her Pokémon, but other trainers' too.

He knew he was talking places like Professor Oak's ranch being destroyed, likely no care if the man was inside or not.

A frightened mewl from Beta could be heard, feeling her press her head into him, placing his free hand around her, ignoring any odd stares sent his way.

He didn't care, he knew how the poor thing felt, forcing himself to remain strong for her, knowing he couldn't break, not even after this meeting ends. No, both of the clones are going to be distraught from this and need shoulders to cry on.

He wouldn't even be surprised if Butch and Cassidy came running in sometime later about this whole thing.

If the roles were reversed, he probably would do the same thing to them…

He barely focused on whatever else Giovanni said, his mind still reeling over the fact that what he's potentially suggesting might start a full scale war.

If they surround that city and attack it with Darkness' minions, hundreds of civilians are going to get killed. Those representing the gyms and leagues might end up killed or seriously wounded, their Pokémon especially.

When the meeting eventually ended, everyone allowed to return to whatever they were do prior.

In less than two weeks, all the Rockets would be packed and transferred, shown who their squad leaders are and given plans.

Sebastian wasn't sure what to expect, but knew something had to be done soon or else he'll end up losing everything he loves.

Unconsciously, he wrapped his hand around the hidden pendant, giving a silent prayer to Dialga or any deity that may listen.

He prayed he'll think of something to save himself and his family, that Panthera may save them from this hell.

* * *

 _ **Sorry if this chapter is rushed, had gotten nearly 16 chapters done ahead of time when I first started, then writer's block struck as per-usual.**_

 _ **Thankfully, due to writing ahead so much and posting once a week, it gave me time to try and work around out. Sure enough, did so, but then it struck again, so again, really sorry if its rushed. I didn't want to drag it on to long and end it where it'll lead to another fanfic I'm working on. Right now it's being edited, but hopefully I'll get enough done to start posting... Once I think of a good title for it that is...**_

 _ **But because of it, I'm open to any and all ideas to clean this chapter up and I sincerely hope you've enjoyed reading Project Beta and Omega.**_

 _ **Please read and review**_


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